From 4734f32a1c418c7c2b91813f0cea3065d30111ec Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 18 Nov 2019 14:07:56 +0100
Subject: [PATCH] version 0.4.0

---
 .gitmodules                                   |   3 -
 CHANGELOG.md                                  |  13 ++
 README.md                                     |   1 +
 src/.conda_envs                               |   1 +
 src/.conda_packages.sh                        | 149 ++++++++++++++++++
 src/.conda_psmn.sh                            |   1 +
 .../bcftools/1.7/Dockerfile                   |   0
 .../bcftools/1.7/docker_init.sh               |   2 +
 .../bedtools/2.25.0/Dockerfile                |   0
 .../bedtools/2.25.0/docker_init.sh            |   2 +
 .../bioawk/1.0/Dockerfile                     |   0
 src/.docker_modules/bioawk/1.0/docker_init.sh |   2 +
 .../bowtie/1.2.2/Dockerfile                   |   0
 .../bowtie/1.2.2/docker_init.sh               |   2 +
 .../bowtie2/2.3.4.1/Dockerfile                |   0
 .../bowtie2/2.3.4.1/docker_init.sh            |   2 +
 .../bwa/0.7.17/Dockerfile                     |   0
 src/.docker_modules/bwa/0.7.17/docker_init.sh |   2 +
 .../canu/1.6/Dockerfile                       |   0
 src/.docker_modules/canu/1.6/docker_init.sh   |   2 +
 .../cutadapt/1.14/Dockerfile                  |   0
 .../cutadapt/1.14/docker_init.sh              |   2 +
 .../cutadapt/1.15/Dockerfile                  |   0
 .../cutadapt/1.15/docker_init.sh              |   2 +
 .../cutadapt/2.1/Dockerfile                   |   0
 .../cutadapt/2.1/docker_init.sh               |   2 +
 .../deeptools/3.0.2/Dockerfile                |   0
 .../deeptools/3.0.2/docker_init.sh            |   2 +
 .../deeptools/3.1.1/Dockerfile                |   0
 .../deeptools/3.1.1/docker_init.sh            |   2 +
 src/.docker_modules/docker_push.sh            |   2 +
 src/.docker_modules/docker_update.sh          |   2 +
 .../fastp/0.19.7/Dockerfile                   |   0
 .../fastp/0.19.7/docker_init.sh               |   2 +
 .../fastqc/0.11.5/Dockerfile                  |   0
 .../fastqc/0.11.5/docker_init.sh              |   2 +
 .../file_handle/0.1.1/Dockerfile              |   0
 .../file_handle/0.1.1/docker_init.sh          |   2 +
 .../gatk/4.0.8.1/Dockerfile                   |   0
 .../gatk/4.0.8.1/docker_init.sh               |   2 +
 .../hisat2/2.0.0/Dockerfile                   |   0
 .../hisat2/2.0.0/docker_init.sh               |   2 +
 .../hisat2/2.1.0/Dockerfile                   |   0
 .../hisat2/2.1.0/docker_init.sh               |   2 +
 .../htseq/0.11.2/Dockerfile                   |   0
 .../htseq/0.11.2/docker_init.sh               |   2 +
 .../htseq/0.8.0/Dockerfile                    |   0
 .../htseq/0.8.0/docker_init.sh                |   2 +
 .../kallisto/0.43.1/Dockerfile                |   0
 .../kallisto/0.43.1/docker_init.sh            |   2 +
 .../kallisto/0.44.0/Dockerfile                |   0
 .../kallisto/0.44.0/docker_init.sh            |   2 +
 .../macs2/2.1.2/Dockerfile                    |   0
 .../macs2/2.1.2/docker_init.sh                |   2 +
 .../multiqc/1.0/Dockerfile                    |   0
 .../multiqc/1.0/docker_init.sh                |   2 +
 .../multiqc/1.7/Dockerfile                    |   0
 .../multiqc/1.7/docker_init.sh                |   2 +
 .../music/6613c53/Dockerfile                  |   0
 .../music/6613c53/docker_init.sh              |   2 +
 .../picard/2.18.11/Dockerfile                 |   0
 .../picard/2.18.11/PicardCommandLine          |   0
 .../picard/2.18.11/docker_init.sh             |   2 +
 .../pigz/2.4/Dockerfile                       |   0
 src/.docker_modules/pigz/2.4/docker_init.sh   |   2 +
 .../python/3.8/Dockerfile                     |   0
 src/.docker_modules/python/3.8/docker_init.sh |   2 +
 .../r/3.5.3/Dockerfile                        |   0
 src/.docker_modules/r/3.5.3/docker_init.sh    |   2 +
 .../rsem/1.3.0/Dockerfile                     |   0
 src/.docker_modules/rsem/1.3.0/docker_init.sh |   2 +
 .../salmon/0.8.2/Dockerfile                   |   0
 .../salmon/0.8.2/docker_init.sh               |   2 +
 .../sambamba/0.6.7/Dockerfile                 |   0
 .../sambamba/0.6.7/docker_init.sh             |   2 +
 .../sambamba/0.6.9/Dockerfile                 |   0
 .../sambamba/0.6.9/docker_init.sh             |   2 +
 .../samblaster/0.1.24/Dockerfile              |   0
 .../samblaster/0.1.24/docker_init.sh          |   2 +
 .../samtools/1.7/Dockerfile                   |   0
 .../samtools/1.7/docker_init.sh               |   2 +
 .../sratoolkit/2.8.2/Dockerfile               |   0
 .../sratoolkit/2.8.2/docker_init.sh           |   2 +
 .../subread/1.6.4/Dockerfile                  |   0
 .../subread/1.6.4/docker_init.sh              |   2 +
 .../tophat/2.1.1/Dockerfile                   |   0
 .../tophat/2.1.1/docker_init.sh               |   2 +
 .../trimmomatic/0.36/Dockerfile               |   0
 .../trimmomatic/0.36/docker_init.sh           |   2 +
 .../ucsc/375/Dockerfile                       |   0
 src/.docker_modules/ucsc/375/docker_init.sh   |   2 +
 .../umi_tools/0.5.4/Dockerfile                |   0
 .../umi_tools/0.5.4/docker_init.sh            |   2 +
 .../umi_tools/1.0.0/Dockerfile                |   0
 .../umi_tools/1.0.0/docker_init.sh            |   2 +
 .../urqt/d62c1f8/Dockerfile                   |   0
 .../urqt/d62c1f8/docker_init.sh               |   2 +
 .../bcftools/1.7/bcftools                     |   0
 .../bcftools/1.7/bcftools.def                 |   0
 .../bcftools/1.7/build.sh                     |   0
 .../bedtools/2.25.0/bedtools                  |   0
 .../bedtools/2.25.0/bedtools.def              |   0
 .../bedtools/2.25.0/build.sh                  |   0
 .../bioawk/1.0/bioawk                         |   0
 .../bioawk/1.0/bioawk.def                     |   0
 .../bioawk/1.0/build.sh                       |   0
 .../bowtie/1.2.2/bowtie                       |   0
 .../bowtie/1.2.2/bowtie.def                   |   0
 .../bowtie/1.2.2/build.sh                     |   0
 .../bowtie2/2.3.4.1/bowtie2                   |   0
 .../bowtie2/2.3.4.1/bowtie2.def               |   0
 .../bowtie2/2.3.4.1/build.sh                  |   0
 .../bwa/0.7.17/build.sh                       |   0
 .../bwa/0.7.17/bwa                            |   0
 .../bwa/0.7.17/bwa.def                        |   0
 .../canu/1.6/build.sh                         |   0
 .../canu/1.6/canu                             |   0
 .../canu/1.6/canu.def                         |   0
 .../cutadapt/1.14/build.sh                    |   0
 .../cutadapt/1.14/cutadapt                    |   0
 .../cutadapt/1.14/cutadapt.def                |   0
 .../cutadapt/1.15/build.sh                    |   0
 .../cutadapt/1.15/cutadapt                    |   0
 .../cutadapt/1.15/cutadapt.def                |   0
 .../cutadapt/2.1/build.sh                     |   0
 .../cutadapt/2.1/cutadapt                     |   0
 .../cutadapt/2.1/cutadapt.def                 |   0
 .../deeptools/3.0.2/build.sh                  |   0
 .../deeptools/3.0.2/deeptools                 |   0
 .../deeptools/3.0.2/deeptools.def             |   0
 .../deeptools/3.1.1/build.sh                  |   0
 .../deeptools/3.1.1/deeptools                 |   0
 .../deeptools/3.1.1/deeptools.def             |   0
 .../docker_to_singularity.sh                  |   0
 .../fastp/0.19.7/build.sh                     |   0
 .../fastp/0.19.7/fastp                        |   0
 .../fastp/0.19.7/fastp.def                    |   0
 .../fastqc/0.11.5/build.sh                    |   0
 .../fastqc/0.11.5/fastqc                      |   0
 .../fastqc/0.11.5/fastqc.def                  |   0
 .../file_handle/0.1.1/build.sh                |   0
 .../file_handle/0.1.1/file_handle             |   0
 .../file_handle/0.1.1/file_handle.def         |   0
 .../gatk/4.0.8.1/build.sh                     |   0
 .../gatk/4.0.8.1/gatk                         |   0
 .../gatk/4.0.8.1/gatk.def                     |   0
 .../hisat2/2.0.0/build.sh                     |   0
 .../hisat2/2.0.0/hisat2                       |   0
 .../hisat2/2.0.0/hisat2.def                   |   0
 .../hisat2/2.1.0/build.sh                     |   0
 .../hisat2/2.1.0/hisat2                       |   0
 .../hisat2/2.1.0/hisat2.def                   |   0
 .../htseq/0.11.2/build.sh                     |   0
 .../htseq/0.11.2/htseq                        |   0
 .../htseq/0.11.2/htseq.def                    |   0
 .../htseq/0.8.0/build.sh                      |   0
 .../htseq/0.8.0/htseq                         |   0
 .../htseq/0.8.0/htseq.def                     |   0
 .../kallisto/0.43.1/build.sh                  |   0
 .../kallisto/0.43.1/kallisto                  |   0
 .../kallisto/0.43.1/kallisto.def              |   0
 .../kallisto/0.44.0/build.sh                  |   0
 .../kallisto/0.44.0/kallisto                  |   0
 .../kallisto/0.44.0/kallisto.def              |   0
 .../macs2/2.1.2/build.sh                      |   0
 .../macs2/2.1.2/macs2                         |   0
 .../macs2/2.1.2/macs2.def                     |   0
 .../multiqc/1.0/build.sh                      |   0
 .../multiqc/1.0/multiqc                       |   0
 .../multiqc/1.0/multiqc.def                   |   0
 .../multiqc/1.7/build.sh                      |   0
 .../multiqc/1.7/multiqc                       |   0
 .../multiqc/1.7/multiqc.def                   |   0
 .../music/6613c53/build.sh                    |   0
 .../music/6613c53/music                       |   0
 .../music/6613c53/music.def                   |   0
 .../picard/2.18.11/PicardCommandLine          |   0
 .../picard/2.18.11/build.sh                   |   0
 .../picard/2.18.11/picard                     |   0
 .../picard/2.18.11/picard.def                 |   0
 .../pigz/2.4/build.sh                         |   0
 .../pigz/2.4/pigz                             |   0
 .../pigz/2.4/pigz.def                         |   0
 .../r/3.5.3/build.sh                          |   0
 .../r/3.5.3/r                                 |   0
 .../r/3.5.3/r.def                             |   0
 .../rsem/1.3.0/build.sh                       |   0
 .../rsem/1.3.0/rsem                           |   0
 .../rsem/1.3.0/rsem.def                       |   0
 .../salmon/0.8.2/build.sh                     |   0
 .../salmon/0.8.2/salmon                       |   0
 .../salmon/0.8.2/salmon.def                   |   0
 .../sambamba/0.6.7/build.sh                   |   0
 .../sambamba/0.6.7/sambamba                   |   0
 .../sambamba/0.6.7/sambamba.def               |   0
 .../sambamba/0.6.9/build.sh                   |   0
 .../sambamba/0.6.9/sambamba                   |   0
 .../sambamba/0.6.9/sambamba.def               |   0
 .../samblaster/0.1.24/build.sh                |   0
 .../samblaster/0.1.24/samblaster              |   0
 .../samblaster/0.1.24/samblaster.def          |   0
 .../samtools/1.7/build.sh                     |   0
 .../samtools/1.7/samtools                     |   0
 .../samtools/1.7/samtools.def                 |   0
 .../sratoolkit/2.8.2/build.sh                 |   0
 .../sratoolkit/2.8.2/sratoolkit               |   0
 .../sratoolkit/2.8.2/sratoolkit.def           |   0
 .../subread/1.6.4/build.sh                    |   0
 .../subread/1.6.4/subread                     |   0
 .../subread/1.6.4/subread.def                 |   0
 .../tophat/2.1.1/build.sh                     |   0
 .../tophat/2.1.1/tophat                       |   0
 .../tophat/2.1.1/tophat.def                   |   0
 .../trimmomatic/0.36/build.sh                 |   0
 .../trimmomatic/0.36/trimmomatic              |   0
 .../trimmomatic/0.36/trimmomatic.def          |   0
 .../ucsc/375/build.sh                         |   0
 .../ucsc/375/ucsc                             |   0
 .../ucsc/375/ucsc.def                         |   0
 .../umi_tools/1.0.0/build.sh                  |   0
 .../umi_tools/1.0.0/umi_tools                 |   0
 .../umi_tools/1.0.0/umi_tools.def             |   0
 .../urqt/d62c1f8/build.sh                     |   0
 .../urqt/d62c1f8/urqt                         |   0
 .../urqt/d62c1f8/urqt.def                     |   0
 src/.update_config.sh                         |  18 +++
 src/{update_tools.sh => .update_tools.sh}     |   0
 src/conda_packages.sh                         |  61 -------
 .../bcftools/1.7/docker_init.sh               |   2 -
 .../bedtools/2.25.0/docker_init.sh            |   2 -
 src/docker_modules/bioawk/1.0/docker_init.sh  |   2 -
 .../bowtie/1.2.2/docker_init.sh               |   2 -
 .../bowtie2/2.3.4.1/docker_init.sh            |   2 -
 src/docker_modules/bwa/0.7.17/docker_init.sh  |   2 -
 src/docker_modules/canu/1.6/docker_init.sh    |   2 -
 .../cutadapt/1.14/docker_init.sh              |   2 -
 .../cutadapt/1.15/docker_init.sh              |   2 -
 .../cutadapt/2.1/docker_init.sh               |   2 -
 .../deeptools/3.0.2/docker_init.sh            |   2 -
 .../deeptools/3.1.1/docker_init.sh            |   2 -
 .../fastp/0.19.7/docker_init.sh               |   2 -
 .../fastqc/0.11.5/docker_init.sh              |   2 -
 .../file_handle/0.1.1/docker_init.sh          |   2 -
 .../gatk/4.0.8.1/docker_init.sh               |   2 -
 .../hisat2/2.0.0/docker_init.sh               |   2 -
 .../hisat2/2.1.0/docker_init.sh               |   2 -
 .../htseq/0.11.2/docker_init.sh               |   2 -
 src/docker_modules/htseq/0.8.0/docker_init.sh |   2 -
 .../kallisto/0.43.1/docker_init.sh            |   2 -
 .../kallisto/0.44.0/docker_init.sh            |   2 -
 src/docker_modules/macs2/2.1.2/docker_init.sh |   2 -
 src/docker_modules/multiqc/1.0/docker_init.sh |   2 -
 src/docker_modules/multiqc/1.7/docker_init.sh |   2 -
 .../music/6613c53/docker_init.sh              |   2 -
 .../picard/2.18.11/docker_init.sh             |   2 -
 src/docker_modules/pigz/2.4/docker_init.sh    |   2 -
 src/docker_modules/python/3.8/docker_init.sh  |   2 -
 src/docker_modules/r/3.5.3/docker_init.sh     |   2 -
 src/docker_modules/rsem/1.3.0/docker_init.sh  |   2 -
 .../salmon/0.8.2/docker_init.sh               |   2 -
 .../sambamba/0.6.7/docker_init.sh             |   2 -
 .../sambamba/0.6.9/docker_init.sh             |   2 -
 .../samblaster/0.1.24/docker_init.sh          |   2 -
 .../samtools/1.7/docker_init.sh               |   2 -
 .../sratoolkit/2.8.2/docker_init.sh           |   2 -
 .../subread/1.6.4/docker_init.sh              |   2 -
 .../tophat/2.1.1/docker_init.sh               |   2 -
 .../trimmomatic/0.36/docker_init.sh           |   2 -
 src/docker_modules/ucsc/375/docker_init.sh    |   2 -
 .../umi_tools/0.5.4/docker_init.sh            |   2 -
 .../umi_tools/1.0.0/docker_init.sh            |   2 -
 .../urqt/d62c1f8/docker_init.sh               |   2 -
 src/{kallisto_index.pbs => in2p3.pbs}         |   0
 src/nf_modules/bedtools/fasta_from_bed.config |  28 +---
 src/nf_modules/bowtie/indexing.config         |  28 +---
 src/nf_modules/bowtie/mapping_paired.config   |  28 +---
 src/nf_modules/bowtie/mapping_single.config   |  28 +---
 src/nf_modules/bowtie2/indexing.config        |  28 +---
 src/nf_modules/bowtie2/mapping_paired.config  |  28 +---
 src/nf_modules/bowtie2/mapping_single.config  |  28 +---
 src/nf_modules/bwa/indexing.config            |  28 +---
 src/nf_modules/bwa/mapping_paired.config      |  28 +---
 .../cutadapt/adaptor_removal_paired.config    |  28 +---
 .../cutadapt/adaptor_removal_single.config    |  28 +---
 .../cutadapt/trimming_paired.config           |  27 +---
 .../cutadapt/trimming_single.config           |  27 +---
 src/nf_modules/deeptools/bam_to_bigwig.config |  46 ++----
 .../deeptools/compute_matrix.config           |  28 +---
 src/nf_modules/deeptools/plot_profile.config  |  28 +---
 src/nf_modules/fastp/fastp_paired.config      |  28 +---
 src/nf_modules/fastp/fastp_single.config      |  28 +---
 src/nf_modules/fastqc/fastqc_paired.config    |  28 +---
 src/nf_modules/fastqc/fastqc_single.config    |  28 +---
 src/nf_modules/hisat2/indexing.config         |  28 +---
 src/nf_modules/hisat2/mapping_paired.config   |  24 +--
 src/nf_modules/hisat2/mapping_single.config   |  24 +--
 src/nf_modules/htseq/htseq.config             |  46 ++----
 src/nf_modules/kallisto/indexing.config       |  28 +---
 src/nf_modules/kallisto/mapping_paired.config |  28 +---
 src/nf_modules/kallisto/mapping_single.config |  28 +---
 src/nf_modules/macs2/peak_calling.config      |  28 +---
 src/nf_modules/multiqc/multiqc_paired.config  |  46 ++----
 src/nf_modules/multiqc/multiqc_single.config  |  46 ++----
 .../music/peak_calling_single.config          |  64 ++------
 src/nf_modules/rsem/indexing.config           |  28 +---
 .../rsem/quantification_paired.config         |  28 +---
 .../rsem/quantification_single.config         |  28 +---
 src/nf_modules/sambamba/index_bams.config     |  28 +---
 src/nf_modules/sambamba/sort_bams.config      |  28 +---
 src/nf_modules/sambamba/split_bams.config     |  28 +---
 src/nf_modules/samblaster/dedup_sams.config   |  28 +---
 src/nf_modules/samtools/filter_bams.config    |  28 +---
 src/nf_modules/samtools/index_bams.config     |  28 +---
 src/nf_modules/samtools/sort_bams.config      |  28 +---
 src/nf_modules/samtools/split_bams.config     |  28 +---
 src/nf_modules/sratoolkit/fastqdump.config    |  28 +---
 src/nf_modules/subread/subread.config         |  46 ++----
 src/nf_modules/urqt/trimming_paired.config    |  28 +---
 src/nf_modules/urqt/trimming_single.config    |  28 +---
 src/psmn_modules                              |   1 -
 src/training_dataset.config                   |  97 ++++++------
 321 files changed, 663 insertions(+), 1266 deletions(-)
 create mode 120000 src/.conda_envs
 create mode 100644 src/.conda_packages.sh
 create mode 120000 src/.conda_psmn.sh
 rename src/{docker_modules => .docker_modules}/bcftools/1.7/Dockerfile (100%)
 create mode 100755 src/.docker_modules/bcftools/1.7/docker_init.sh
 rename src/{docker_modules => .docker_modules}/bedtools/2.25.0/Dockerfile (100%)
 create mode 100755 src/.docker_modules/bedtools/2.25.0/docker_init.sh
 rename src/{docker_modules => .docker_modules}/bioawk/1.0/Dockerfile (100%)
 create mode 100755 src/.docker_modules/bioawk/1.0/docker_init.sh
 rename src/{docker_modules => .docker_modules}/bowtie/1.2.2/Dockerfile (100%)
 create mode 100755 src/.docker_modules/bowtie/1.2.2/docker_init.sh
 rename src/{docker_modules => .docker_modules}/bowtie2/2.3.4.1/Dockerfile (100%)
 create mode 100755 src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh
 rename src/{docker_modules => .docker_modules}/bwa/0.7.17/Dockerfile (100%)
 create mode 100755 src/.docker_modules/bwa/0.7.17/docker_init.sh
 rename src/{docker_modules => .docker_modules}/canu/1.6/Dockerfile (100%)
 create mode 100755 src/.docker_modules/canu/1.6/docker_init.sh
 rename src/{docker_modules => .docker_modules}/cutadapt/1.14/Dockerfile (100%)
 create mode 100755 src/.docker_modules/cutadapt/1.14/docker_init.sh
 rename src/{docker_modules => .docker_modules}/cutadapt/1.15/Dockerfile (100%)
 create mode 100755 src/.docker_modules/cutadapt/1.15/docker_init.sh
 rename src/{docker_modules => .docker_modules}/cutadapt/2.1/Dockerfile (100%)
 create mode 100755 src/.docker_modules/cutadapt/2.1/docker_init.sh
 rename src/{docker_modules => .docker_modules}/deeptools/3.0.2/Dockerfile (100%)
 create mode 100755 src/.docker_modules/deeptools/3.0.2/docker_init.sh
 rename src/{docker_modules => .docker_modules}/deeptools/3.1.1/Dockerfile (100%)
 create mode 100755 src/.docker_modules/deeptools/3.1.1/docker_init.sh
 create mode 100755 src/.docker_modules/docker_push.sh
 create mode 100644 src/.docker_modules/docker_update.sh
 rename src/{docker_modules => .docker_modules}/fastp/0.19.7/Dockerfile (100%)
 create mode 100755 src/.docker_modules/fastp/0.19.7/docker_init.sh
 rename src/{docker_modules => .docker_modules}/fastqc/0.11.5/Dockerfile (100%)
 create mode 100755 src/.docker_modules/fastqc/0.11.5/docker_init.sh
 rename src/{docker_modules => .docker_modules}/file_handle/0.1.1/Dockerfile (100%)
 create mode 100755 src/.docker_modules/file_handle/0.1.1/docker_init.sh
 rename src/{docker_modules => .docker_modules}/gatk/4.0.8.1/Dockerfile (100%)
 create mode 100755 src/.docker_modules/gatk/4.0.8.1/docker_init.sh
 rename src/{docker_modules => .docker_modules}/hisat2/2.0.0/Dockerfile (100%)
 create mode 100755 src/.docker_modules/hisat2/2.0.0/docker_init.sh
 rename src/{docker_modules => .docker_modules}/hisat2/2.1.0/Dockerfile (100%)
 create mode 100755 src/.docker_modules/hisat2/2.1.0/docker_init.sh
 rename src/{docker_modules => .docker_modules}/htseq/0.11.2/Dockerfile (100%)
 create mode 100755 src/.docker_modules/htseq/0.11.2/docker_init.sh
 rename src/{docker_modules => .docker_modules}/htseq/0.8.0/Dockerfile (100%)
 create mode 100755 src/.docker_modules/htseq/0.8.0/docker_init.sh
 rename src/{docker_modules => .docker_modules}/kallisto/0.43.1/Dockerfile (100%)
 create mode 100755 src/.docker_modules/kallisto/0.43.1/docker_init.sh
 rename src/{docker_modules => .docker_modules}/kallisto/0.44.0/Dockerfile (100%)
 create mode 100755 src/.docker_modules/kallisto/0.44.0/docker_init.sh
 rename src/{docker_modules => .docker_modules}/macs2/2.1.2/Dockerfile (100%)
 create mode 100755 src/.docker_modules/macs2/2.1.2/docker_init.sh
 rename src/{docker_modules => .docker_modules}/multiqc/1.0/Dockerfile (100%)
 create mode 100755 src/.docker_modules/multiqc/1.0/docker_init.sh
 rename src/{docker_modules => .docker_modules}/multiqc/1.7/Dockerfile (100%)
 create mode 100755 src/.docker_modules/multiqc/1.7/docker_init.sh
 rename src/{docker_modules => .docker_modules}/music/6613c53/Dockerfile (100%)
 create mode 100755 src/.docker_modules/music/6613c53/docker_init.sh
 rename src/{docker_modules => .docker_modules}/picard/2.18.11/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/picard/2.18.11/PicardCommandLine (100%)
 create mode 100755 src/.docker_modules/picard/2.18.11/docker_init.sh
 rename src/{docker_modules => .docker_modules}/pigz/2.4/Dockerfile (100%)
 create mode 100755 src/.docker_modules/pigz/2.4/docker_init.sh
 rename src/{docker_modules => .docker_modules}/python/3.8/Dockerfile (100%)
 create mode 100755 src/.docker_modules/python/3.8/docker_init.sh
 rename src/{docker_modules => .docker_modules}/r/3.5.3/Dockerfile (100%)
 create mode 100755 src/.docker_modules/r/3.5.3/docker_init.sh
 rename src/{docker_modules => .docker_modules}/rsem/1.3.0/Dockerfile (100%)
 create mode 100755 src/.docker_modules/rsem/1.3.0/docker_init.sh
 rename src/{docker_modules => .docker_modules}/salmon/0.8.2/Dockerfile (100%)
 create mode 100755 src/.docker_modules/salmon/0.8.2/docker_init.sh
 rename src/{docker_modules => .docker_modules}/sambamba/0.6.7/Dockerfile (100%)
 create mode 100755 src/.docker_modules/sambamba/0.6.7/docker_init.sh
 rename src/{docker_modules => .docker_modules}/sambamba/0.6.9/Dockerfile (100%)
 create mode 100755 src/.docker_modules/sambamba/0.6.9/docker_init.sh
 rename src/{docker_modules => .docker_modules}/samblaster/0.1.24/Dockerfile (100%)
 create mode 100755 src/.docker_modules/samblaster/0.1.24/docker_init.sh
 rename src/{docker_modules => .docker_modules}/samtools/1.7/Dockerfile (100%)
 create mode 100755 src/.docker_modules/samtools/1.7/docker_init.sh
 rename src/{docker_modules => .docker_modules}/sratoolkit/2.8.2/Dockerfile (100%)
 create mode 100755 src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
 rename src/{docker_modules => .docker_modules}/subread/1.6.4/Dockerfile (100%)
 create mode 100755 src/.docker_modules/subread/1.6.4/docker_init.sh
 rename src/{docker_modules => .docker_modules}/tophat/2.1.1/Dockerfile (100%)
 create mode 100755 src/.docker_modules/tophat/2.1.1/docker_init.sh
 rename src/{docker_modules => .docker_modules}/trimmomatic/0.36/Dockerfile (100%)
 create mode 100755 src/.docker_modules/trimmomatic/0.36/docker_init.sh
 rename src/{docker_modules => .docker_modules}/ucsc/375/Dockerfile (100%)
 create mode 100755 src/.docker_modules/ucsc/375/docker_init.sh
 rename src/{docker_modules => .docker_modules}/umi_tools/0.5.4/Dockerfile (100%)
 create mode 100755 src/.docker_modules/umi_tools/0.5.4/docker_init.sh
 rename src/{docker_modules => .docker_modules}/umi_tools/1.0.0/Dockerfile (100%)
 create mode 100755 src/.docker_modules/umi_tools/1.0.0/docker_init.sh
 rename src/{docker_modules => .docker_modules}/urqt/d62c1f8/Dockerfile (100%)
 create mode 100755 src/.docker_modules/urqt/d62c1f8/docker_init.sh
 rename src/{singularity_modules => .singularity_modules}/bcftools/1.7/bcftools (100%)
 rename src/{singularity_modules => .singularity_modules}/bcftools/1.7/bcftools.def (100%)
 rename src/{singularity_modules => .singularity_modules}/bcftools/1.7/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/bedtools/2.25.0/bedtools (100%)
 rename src/{singularity_modules => .singularity_modules}/bedtools/2.25.0/bedtools.def (100%)
 rename src/{singularity_modules => .singularity_modules}/bedtools/2.25.0/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/bioawk/1.0/bioawk (100%)
 rename src/{singularity_modules => .singularity_modules}/bioawk/1.0/bioawk.def (100%)
 rename src/{singularity_modules => .singularity_modules}/bioawk/1.0/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/bowtie/1.2.2/bowtie (100%)
 rename src/{singularity_modules => .singularity_modules}/bowtie/1.2.2/bowtie.def (100%)
 rename src/{singularity_modules => .singularity_modules}/bowtie/1.2.2/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/bowtie2/2.3.4.1/bowtie2 (100%)
 rename src/{singularity_modules => .singularity_modules}/bowtie2/2.3.4.1/bowtie2.def (100%)
 rename src/{singularity_modules => .singularity_modules}/bowtie2/2.3.4.1/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/bwa/0.7.17/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/bwa/0.7.17/bwa (100%)
 rename src/{singularity_modules => .singularity_modules}/bwa/0.7.17/bwa.def (100%)
 rename src/{singularity_modules => .singularity_modules}/canu/1.6/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/canu/1.6/canu (100%)
 rename src/{singularity_modules => .singularity_modules}/canu/1.6/canu.def (100%)
 rename src/{singularity_modules => .singularity_modules}/cutadapt/1.14/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/cutadapt/1.14/cutadapt (100%)
 rename src/{singularity_modules => .singularity_modules}/cutadapt/1.14/cutadapt.def (100%)
 rename src/{singularity_modules => .singularity_modules}/cutadapt/1.15/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/cutadapt/1.15/cutadapt (100%)
 rename src/{singularity_modules => .singularity_modules}/cutadapt/1.15/cutadapt.def (100%)
 rename src/{singularity_modules => .singularity_modules}/cutadapt/2.1/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/cutadapt/2.1/cutadapt (100%)
 rename src/{singularity_modules => .singularity_modules}/cutadapt/2.1/cutadapt.def (100%)
 rename src/{singularity_modules => .singularity_modules}/deeptools/3.0.2/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/deeptools/3.0.2/deeptools (100%)
 rename src/{singularity_modules => .singularity_modules}/deeptools/3.0.2/deeptools.def (100%)
 rename src/{singularity_modules => .singularity_modules}/deeptools/3.1.1/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/deeptools/3.1.1/deeptools (100%)
 rename src/{singularity_modules => .singularity_modules}/deeptools/3.1.1/deeptools.def (100%)
 rename src/{singularity_modules => .singularity_modules}/docker_to_singularity.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/fastp/0.19.7/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/fastp/0.19.7/fastp (100%)
 rename src/{singularity_modules => .singularity_modules}/fastp/0.19.7/fastp.def (100%)
 rename src/{singularity_modules => .singularity_modules}/fastqc/0.11.5/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/fastqc/0.11.5/fastqc (100%)
 rename src/{singularity_modules => .singularity_modules}/fastqc/0.11.5/fastqc.def (100%)
 rename src/{singularity_modules => .singularity_modules}/file_handle/0.1.1/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/file_handle/0.1.1/file_handle (100%)
 rename src/{singularity_modules => .singularity_modules}/file_handle/0.1.1/file_handle.def (100%)
 rename src/{singularity_modules => .singularity_modules}/gatk/4.0.8.1/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/gatk/4.0.8.1/gatk (100%)
 rename src/{singularity_modules => .singularity_modules}/gatk/4.0.8.1/gatk.def (100%)
 rename src/{singularity_modules => .singularity_modules}/hisat2/2.0.0/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/hisat2/2.0.0/hisat2 (100%)
 rename src/{singularity_modules => .singularity_modules}/hisat2/2.0.0/hisat2.def (100%)
 rename src/{singularity_modules => .singularity_modules}/hisat2/2.1.0/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/hisat2/2.1.0/hisat2 (100%)
 rename src/{singularity_modules => .singularity_modules}/hisat2/2.1.0/hisat2.def (100%)
 rename src/{singularity_modules => .singularity_modules}/htseq/0.11.2/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/htseq/0.11.2/htseq (100%)
 rename src/{singularity_modules => .singularity_modules}/htseq/0.11.2/htseq.def (100%)
 rename src/{singularity_modules => .singularity_modules}/htseq/0.8.0/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/htseq/0.8.0/htseq (100%)
 rename src/{singularity_modules => .singularity_modules}/htseq/0.8.0/htseq.def (100%)
 rename src/{singularity_modules => .singularity_modules}/kallisto/0.43.1/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/kallisto/0.43.1/kallisto (100%)
 rename src/{singularity_modules => .singularity_modules}/kallisto/0.43.1/kallisto.def (100%)
 rename src/{singularity_modules => .singularity_modules}/kallisto/0.44.0/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/kallisto/0.44.0/kallisto (100%)
 rename src/{singularity_modules => .singularity_modules}/kallisto/0.44.0/kallisto.def (100%)
 rename src/{singularity_modules => .singularity_modules}/macs2/2.1.2/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/macs2/2.1.2/macs2 (100%)
 rename src/{singularity_modules => .singularity_modules}/macs2/2.1.2/macs2.def (100%)
 rename src/{singularity_modules => .singularity_modules}/multiqc/1.0/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/multiqc/1.0/multiqc (100%)
 rename src/{singularity_modules => .singularity_modules}/multiqc/1.0/multiqc.def (100%)
 rename src/{singularity_modules => .singularity_modules}/multiqc/1.7/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/multiqc/1.7/multiqc (100%)
 rename src/{singularity_modules => .singularity_modules}/multiqc/1.7/multiqc.def (100%)
 rename src/{singularity_modules => .singularity_modules}/music/6613c53/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/music/6613c53/music (100%)
 rename src/{singularity_modules => .singularity_modules}/music/6613c53/music.def (100%)
 rename src/{singularity_modules => .singularity_modules}/picard/2.18.11/PicardCommandLine (100%)
 rename src/{singularity_modules => .singularity_modules}/picard/2.18.11/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/picard/2.18.11/picard (100%)
 rename src/{singularity_modules => .singularity_modules}/picard/2.18.11/picard.def (100%)
 rename src/{singularity_modules => .singularity_modules}/pigz/2.4/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/pigz/2.4/pigz (100%)
 rename src/{singularity_modules => .singularity_modules}/pigz/2.4/pigz.def (100%)
 rename src/{singularity_modules => .singularity_modules}/r/3.5.3/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/r/3.5.3/r (100%)
 rename src/{singularity_modules => .singularity_modules}/r/3.5.3/r.def (100%)
 rename src/{singularity_modules => .singularity_modules}/rsem/1.3.0/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/rsem/1.3.0/rsem (100%)
 rename src/{singularity_modules => .singularity_modules}/rsem/1.3.0/rsem.def (100%)
 rename src/{singularity_modules => .singularity_modules}/salmon/0.8.2/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/salmon/0.8.2/salmon (100%)
 rename src/{singularity_modules => .singularity_modules}/salmon/0.8.2/salmon.def (100%)
 rename src/{singularity_modules => .singularity_modules}/sambamba/0.6.7/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/sambamba/0.6.7/sambamba (100%)
 rename src/{singularity_modules => .singularity_modules}/sambamba/0.6.7/sambamba.def (100%)
 rename src/{singularity_modules => .singularity_modules}/sambamba/0.6.9/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/sambamba/0.6.9/sambamba (100%)
 rename src/{singularity_modules => .singularity_modules}/sambamba/0.6.9/sambamba.def (100%)
 rename src/{singularity_modules => .singularity_modules}/samblaster/0.1.24/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/samblaster/0.1.24/samblaster (100%)
 rename src/{singularity_modules => .singularity_modules}/samblaster/0.1.24/samblaster.def (100%)
 rename src/{singularity_modules => .singularity_modules}/samtools/1.7/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/samtools/1.7/samtools (100%)
 rename src/{singularity_modules => .singularity_modules}/samtools/1.7/samtools.def (100%)
 rename src/{singularity_modules => .singularity_modules}/sratoolkit/2.8.2/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/sratoolkit/2.8.2/sratoolkit (100%)
 rename src/{singularity_modules => .singularity_modules}/sratoolkit/2.8.2/sratoolkit.def (100%)
 rename src/{singularity_modules => .singularity_modules}/subread/1.6.4/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/subread/1.6.4/subread (100%)
 rename src/{singularity_modules => .singularity_modules}/subread/1.6.4/subread.def (100%)
 rename src/{singularity_modules => .singularity_modules}/tophat/2.1.1/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/tophat/2.1.1/tophat (100%)
 rename src/{singularity_modules => .singularity_modules}/tophat/2.1.1/tophat.def (100%)
 rename src/{singularity_modules => .singularity_modules}/trimmomatic/0.36/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/trimmomatic/0.36/trimmomatic (100%)
 rename src/{singularity_modules => .singularity_modules}/trimmomatic/0.36/trimmomatic.def (100%)
 rename src/{singularity_modules => .singularity_modules}/ucsc/375/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/ucsc/375/ucsc (100%)
 rename src/{singularity_modules => .singularity_modules}/ucsc/375/ucsc.def (100%)
 rename src/{singularity_modules => .singularity_modules}/umi_tools/1.0.0/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/umi_tools/1.0.0/umi_tools (100%)
 rename src/{singularity_modules => .singularity_modules}/umi_tools/1.0.0/umi_tools.def (100%)
 rename src/{singularity_modules => .singularity_modules}/urqt/d62c1f8/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/urqt/d62c1f8/urqt (100%)
 rename src/{singularity_modules => .singularity_modules}/urqt/d62c1f8/urqt.def (100%)
 create mode 100644 src/.update_config.sh
 rename src/{update_tools.sh => .update_tools.sh} (100%)
 delete mode 100644 src/conda_packages.sh
 delete mode 100755 src/docker_modules/bcftools/1.7/docker_init.sh
 delete mode 100755 src/docker_modules/bedtools/2.25.0/docker_init.sh
 delete mode 100755 src/docker_modules/bioawk/1.0/docker_init.sh
 delete mode 100755 src/docker_modules/bowtie/1.2.2/docker_init.sh
 delete mode 100755 src/docker_modules/bowtie2/2.3.4.1/docker_init.sh
 delete mode 100755 src/docker_modules/bwa/0.7.17/docker_init.sh
 delete mode 100755 src/docker_modules/canu/1.6/docker_init.sh
 delete mode 100755 src/docker_modules/cutadapt/1.14/docker_init.sh
 delete mode 100755 src/docker_modules/cutadapt/1.15/docker_init.sh
 delete mode 100755 src/docker_modules/cutadapt/2.1/docker_init.sh
 delete mode 100755 src/docker_modules/deeptools/3.0.2/docker_init.sh
 delete mode 100755 src/docker_modules/deeptools/3.1.1/docker_init.sh
 delete mode 100755 src/docker_modules/fastp/0.19.7/docker_init.sh
 delete mode 100755 src/docker_modules/fastqc/0.11.5/docker_init.sh
 delete mode 100755 src/docker_modules/file_handle/0.1.1/docker_init.sh
 delete mode 100755 src/docker_modules/gatk/4.0.8.1/docker_init.sh
 delete mode 100755 src/docker_modules/hisat2/2.0.0/docker_init.sh
 delete mode 100755 src/docker_modules/hisat2/2.1.0/docker_init.sh
 delete mode 100755 src/docker_modules/htseq/0.11.2/docker_init.sh
 delete mode 100755 src/docker_modules/htseq/0.8.0/docker_init.sh
 delete mode 100755 src/docker_modules/kallisto/0.43.1/docker_init.sh
 delete mode 100755 src/docker_modules/kallisto/0.44.0/docker_init.sh
 delete mode 100755 src/docker_modules/macs2/2.1.2/docker_init.sh
 delete mode 100755 src/docker_modules/multiqc/1.0/docker_init.sh
 delete mode 100755 src/docker_modules/multiqc/1.7/docker_init.sh
 delete mode 100755 src/docker_modules/music/6613c53/docker_init.sh
 delete mode 100755 src/docker_modules/picard/2.18.11/docker_init.sh
 delete mode 100755 src/docker_modules/pigz/2.4/docker_init.sh
 delete mode 100755 src/docker_modules/python/3.8/docker_init.sh
 delete mode 100755 src/docker_modules/r/3.5.3/docker_init.sh
 delete mode 100755 src/docker_modules/rsem/1.3.0/docker_init.sh
 delete mode 100755 src/docker_modules/salmon/0.8.2/docker_init.sh
 delete mode 100755 src/docker_modules/sambamba/0.6.7/docker_init.sh
 delete mode 100755 src/docker_modules/sambamba/0.6.9/docker_init.sh
 delete mode 100755 src/docker_modules/samblaster/0.1.24/docker_init.sh
 delete mode 100755 src/docker_modules/samtools/1.7/docker_init.sh
 delete mode 100755 src/docker_modules/sratoolkit/2.8.2/docker_init.sh
 delete mode 100755 src/docker_modules/subread/1.6.4/docker_init.sh
 delete mode 100755 src/docker_modules/tophat/2.1.1/docker_init.sh
 delete mode 100755 src/docker_modules/trimmomatic/0.36/docker_init.sh
 delete mode 100755 src/docker_modules/ucsc/375/docker_init.sh
 delete mode 100755 src/docker_modules/umi_tools/0.5.4/docker_init.sh
 delete mode 100755 src/docker_modules/umi_tools/1.0.0/docker_init.sh
 delete mode 100755 src/docker_modules/urqt/d62c1f8/docker_init.sh
 rename src/{kallisto_index.pbs => in2p3.pbs} (100%)
 delete mode 160000 src/psmn_modules

diff --git a/.gitmodules b/.gitmodules
index 57a4299e..e69de29b 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +0,0 @@
-[submodule "src/sge_modules"]
-	path = src/psmn_modules
-	url = gitlab_lbmc:PSMN/modules.git
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 94a42d8a..03648b4b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,19 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.4.0] - 2019-11-18
+### Added
+- Add new tools (star,...)
+- conda support at the psmn
+
+## Changed
+- configuration simplification
+- docker and singularity image download instead of local build
+- hidden directories in `src` for project clarity (only `nf_modules` is visible)
+
+## Removed
+- conda support at in2p3 with `-profile in2p3_conda`
+
 ## [0.3.0] - 2019-05-23
 ### Added
 - Add new tools (umi_tools, fastp,...)
diff --git a/README.md b/README.md
index 795d3391..9fbd72fd 100644
--- a/README.md
+++ b/README.md
@@ -8,6 +8,7 @@ To get the last commits from this repository into your fork use the following co
 git remote add upstream gitlab_lbmc:pipelines/nextflow.git
 git pull upstream master
 ```
+If you created your `.config` file before version `0.4.0` you need to run the script `src/.update_config.sh` to use the latest docker, singularity and conda configuration (don't forget to check your config files afterward for typos).
 
 ## Getting Started
 
diff --git a/src/.conda_envs b/src/.conda_envs
new file mode 120000
index 00000000..cf88bffb
--- /dev/null
+++ b/src/.conda_envs
@@ -0,0 +1 @@
+/Xnfs/lbmcdb/common/conda/envs/
\ No newline at end of file
diff --git a/src/.conda_packages.sh b/src/.conda_packages.sh
new file mode 100644
index 00000000..9ac4dfa7
--- /dev/null
+++ b/src/.conda_packages.sh
@@ -0,0 +1,149 @@
+source src/.conda_psmn.sh
+CONDA_ENVS=src/.conda_envs/
+if [ ! -d ${CONDA_ENVS}pigz_2.3.4 ]; then
+  conda create --yes --name pigz_2.3.4 pigz=2.3.4
+fi
+if [ ! -d ${CONDA_ENVS}tophat_2.1.1 ]; then
+  conda create --yes --name tophat_2.1.1 tophat=2.1.1
+fi
+if [ ! -d ${CONDA_ENVS}hisat2_2.0.0 ]; then
+  conda create --yes --name hisat2_2.0.0 hisat2=2.0.0 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}hisat2_2.1.0 ]; then
+  conda create --yes --name hisat2_2.1.0 hisat2=2.1.0 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}rsem_1.3.1 ]; then
+  conda create --yes --name rsem_1.3.1 rsem=1.3.1 samtools=1.3
+fi
+if [ ! -d ${CONDA_ENVS}rsem_1.3.0 ]; then
+  conda create --yes --name rsem_1.3.0 rsem=1.3.0 samtools=1.3
+fi
+if [ ! -d ${CONDA_ENVS}samblaster_0.1.24 ]; then
+  conda create --yes --name samblaster_0.1.24 samblaster=0.1.24
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_0.25.1 ]; then
+  conda create --yes --name nextflow_0.25.1 nextflow=0.25.1
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_19.01.0 ]; then
+  conda create --yes --name nextflow_19.01.0 nextflow=19.01.0
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_0.32.0 ]; then
+  conda create --yes --name nextflow_0.32.0 nextflow=0.32.0
+fi
+if [ ! -d ${CONDA_ENVS}nextflow_0.28.2 ]; then
+  conda create --yes --name nextflow_0.28.2 nextflow=0.28.2
+fi
+if [ ! -d ${CONDA_ENVS}samtools_1.7 ]; then
+  conda create --yes --name samtools_1.7 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}samtools_1.5 ]; then
+  conda create --yes --name samtools_1.5 samtools=1.5
+fi
+if [ ! -d ${CONDA_ENVS}bowtie2_2.3.2 ]; then
+  conda create --yes --name bowtie2_2.3.2 bowtie2=2.3.2 samtools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}bowtie2_2.3.4.1 ]; then
+  conda create --yes --name bowtie2_2.3.4.1 bowtie2=2.3.4.1 samtools=1.7 #&& \
+fi
+if [ ! -d ${CONDA_ENVS}sra-tools_2.8.2 ]; then
+  conda create --yes --name sra-tools_2.8.2 sra-tools=2.8.2
+fi
+if [ ! -d ${CONDA_ENVS}trimmomatic_0.36 ]; then
+  conda create --yes --name trimmomatic_0.36 trimmomatic=0.36
+fi
+if [ ! -d ${CONDA_ENVS}trimmomatic_0.39 ]; then
+  conda create --yes --name trimmomatic_0.39 trimmomatic=0.39
+fi
+if [ ! -d ${CONDA_ENVS}Python_3.6.1 ]; then
+  conda create --yes --name Python_3.6.1 Python=3.6.1
+fi
+if [ ! -d ${CONDA_ENVS}Python_2.7.13 ]; then
+  conda create --yes --name Python_2.7.13 Python=2.7.13
+fi
+if [ ! -d ${CONDA_ENVS}kallisto_0.44.0 ]; then
+  conda create --yes --name kallisto_0.44.0 kallisto=0.44.0
+fi
+if [ ! -d ${CONDA_ENVS}kallisto_0.43.1 ]; then
+  conda create --yes --name kallisto_0.43.1 kallisto=0.43.1
+fi
+if [ ! -d ${CONDA_ENVS}music_1.0.0 ]; then
+  conda create --yes --name music_1.0.0 music=1.0.0
+fi
+if [ ! -d ${CONDA_ENVS}umitools_0.3.4 ]; then
+  conda create --yes --name umitools_0.3.4 umitools=0.3.4
+fi
+if [ ! -d ${CONDA_ENVS}fastp_0.19.7 ]; then
+  conda create --yes --name fastp_0.19.7 fastp=0.19.7
+fi
+if [ ! -d ${CONDA_ENVS}gatk_3.8 ]; then
+  conda create --yes --name gatk_3.8 gatk=3.8
+fi
+if [ ! -d ${CONDA_ENVS}cutadapt_1.14 ]; then
+  conda create --yes --name cutadapt_1.14 cutadapt=1.14
+fi
+if [ ! -d ${CONDA_ENVS}bioawk_1.0 ]; then
+  conda create --yes --name bioawk_1.0 bioawk=1.0
+fi
+if [ ! -d ${CONDA_ENVS}canu_1.7 ]; then
+  conda create --yes --name canu_1.7 canu=1.7
+fi
+if [ ! -d ${CONDA_ENVS}fastqc_0.11.5 ]; then
+  conda create --yes --name fastqc_0.11.5 fastqc=0.11.5
+fi
+if [ ! -d ${CONDA_ENVS}bedtools_2.25.0 ]; then
+  conda create --yes --name bedtools_2.25.0 bedtools=2.25.0
+fi
+if [ ! -d ${CONDA_ENVS}macs2_2.1.2 ]; then
+  conda create --yes --name macs2_2.1.2 macs2=2.1.2
+fi
+if [ ! -d ${CONDA_ENVS}bcftools_1.7 ]; then
+  conda create --yes --name bcftools_1.7 bcftools=1.7
+fi
+if [ ! -d ${CONDA_ENVS}salmon_0.8.2 ]; then
+  conda create --yes --name salmon_0.8.2 salmon=0.8.2
+fi
+if [ ! -d ${CONDA_ENVS}urqt_d62c1f8 ]; then
+  conda create --yes --name urqt_d62c1f8 urqt=d62c1f8
+fi
+if [ ! -d ${CONDA_ENVS}multiqc_0.9 ]; then
+  conda create --yes --name multiqc_0.9 multiqc=0.9
+fi
+if [ ! -d ${CONDA_ENVS}multiqc_1.7 ]; then
+  conda create --yes --name multiqc_1.7 multiqc=1.7
+fi
+if [ ! -d ${CONDA_ENVS}multiqc_1.0 ]; then
+  conda create --yes --name multiqc_1.0 multiqc=1.0
+fi
+if [ ! -d ${CONDA_ENVS}cdhit_4.6.8 ]; then
+  conda create --yes --name cdhit_4.6.8 cdhit=4.6.8
+fi
+if [ ! -d ${CONDA_ENVS}deeptools_3.0.2 ]; then
+  conda create --yes --name deeptools_3.0.2 deeptools=3.0.2
+fi
+if [ ! -d ${CONDA_ENVS}htseq_0.9.1 ]; then
+  conda create --yes --name htseq_0.9.1 htseq=0.9.1
+fi
+if [ ! -d ${CONDA_ENVS}htseq_0.11.2 ]; then
+  conda create --yes --name htseq_0.11.2 htseq=0.11.2
+fi
+if [ ! -d ${CONDA_ENVS}R_3.4.3 ]; then
+  conda create --yes --name R_3.4.3 R=3.4.3
+fi
+if [ ! -d ${CONDA_ENVS}R_3.3.1 ]; then
+  conda create --yes --name R_3.3.1 R=3.3.1
+fi
+if [ ! -d ${CONDA_ENVS}file_handle_0.1.1 ]; then
+  conda create --yes --name file_handle_0.1.1 file_handle=0.1.1
+fi
+if [ ! -d ${CONDA_ENVS}ncdu_1.13 ]; then
+  conda create --yes --name ncdu_1.13 ncdu=1.13
+fi
+if [ ! -d ${CONDA_ENVS}picard_2.18.11 ]; then
+  conda create --yes --name picard_2.18.11 picard=2.18.11
+fi
+if [ ! -d ${CONDA_ENVS}sambamba_0.6.7 ]; then
+  conda create --yes --name sambamba_0.6.7 sambamba=0.6.7
+fi
+if [ ! -d ${CONDA_ENVS}star_2.7.3a ]; then
+  conda create --yes --name star_2.7.3a star=2.7.3a
+fi
diff --git a/src/.conda_psmn.sh b/src/.conda_psmn.sh
new file mode 120000
index 00000000..cbb3d9b5
--- /dev/null
+++ b/src/.conda_psmn.sh
@@ -0,0 +1 @@
+/Xnfs/lbmcdb/common/conda/init.sh
\ No newline at end of file
diff --git a/src/docker_modules/bcftools/1.7/Dockerfile b/src/.docker_modules/bcftools/1.7/Dockerfile
similarity index 100%
rename from src/docker_modules/bcftools/1.7/Dockerfile
rename to src/.docker_modules/bcftools/1.7/Dockerfile
diff --git a/src/.docker_modules/bcftools/1.7/docker_init.sh b/src/.docker_modules/bcftools/1.7/docker_init.sh
new file mode 100755
index 00000000..043a63f0
--- /dev/null
+++ b/src/.docker_modules/bcftools/1.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bcftools/1.7 -t 'lbmc/bcftools:1.7'
diff --git a/src/docker_modules/bedtools/2.25.0/Dockerfile b/src/.docker_modules/bedtools/2.25.0/Dockerfile
similarity index 100%
rename from src/docker_modules/bedtools/2.25.0/Dockerfile
rename to src/.docker_modules/bedtools/2.25.0/Dockerfile
diff --git a/src/.docker_modules/bedtools/2.25.0/docker_init.sh b/src/.docker_modules/bedtools/2.25.0/docker_init.sh
new file mode 100755
index 00000000..37c05b9d
--- /dev/null
+++ b/src/.docker_modules/bedtools/2.25.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bedtools/2.25.0 -t 'lbmc/bedtools:2.25.0'
diff --git a/src/docker_modules/bioawk/1.0/Dockerfile b/src/.docker_modules/bioawk/1.0/Dockerfile
similarity index 100%
rename from src/docker_modules/bioawk/1.0/Dockerfile
rename to src/.docker_modules/bioawk/1.0/Dockerfile
diff --git a/src/.docker_modules/bioawk/1.0/docker_init.sh b/src/.docker_modules/bioawk/1.0/docker_init.sh
new file mode 100755
index 00000000..abbb1e23
--- /dev/null
+++ b/src/.docker_modules/bioawk/1.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bioawk/1.0 -t 'lbmc/bioawk:1.0'
diff --git a/src/docker_modules/bowtie/1.2.2/Dockerfile b/src/.docker_modules/bowtie/1.2.2/Dockerfile
similarity index 100%
rename from src/docker_modules/bowtie/1.2.2/Dockerfile
rename to src/.docker_modules/bowtie/1.2.2/Dockerfile
diff --git a/src/.docker_modules/bowtie/1.2.2/docker_init.sh b/src/.docker_modules/bowtie/1.2.2/docker_init.sh
new file mode 100755
index 00000000..46f45027
--- /dev/null
+++ b/src/.docker_modules/bowtie/1.2.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bowtie/1.2.2 -t 'lbmc/bowtie:1.2.2'
diff --git a/src/docker_modules/bowtie2/2.3.4.1/Dockerfile b/src/.docker_modules/bowtie2/2.3.4.1/Dockerfile
similarity index 100%
rename from src/docker_modules/bowtie2/2.3.4.1/Dockerfile
rename to src/.docker_modules/bowtie2/2.3.4.1/Dockerfile
diff --git a/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh b/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh
new file mode 100755
index 00000000..83cc97d2
--- /dev/null
+++ b/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bowtie2/2.3.4.1 -t 'lbmc/bowtie2:2.3.4.1'
diff --git a/src/docker_modules/bwa/0.7.17/Dockerfile b/src/.docker_modules/bwa/0.7.17/Dockerfile
similarity index 100%
rename from src/docker_modules/bwa/0.7.17/Dockerfile
rename to src/.docker_modules/bwa/0.7.17/Dockerfile
diff --git a/src/.docker_modules/bwa/0.7.17/docker_init.sh b/src/.docker_modules/bwa/0.7.17/docker_init.sh
new file mode 100755
index 00000000..1b1f27f1
--- /dev/null
+++ b/src/.docker_modules/bwa/0.7.17/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/bwa/0.7.17 -t 'lbmc/bwa:0.7.17'
diff --git a/src/docker_modules/canu/1.6/Dockerfile b/src/.docker_modules/canu/1.6/Dockerfile
similarity index 100%
rename from src/docker_modules/canu/1.6/Dockerfile
rename to src/.docker_modules/canu/1.6/Dockerfile
diff --git a/src/.docker_modules/canu/1.6/docker_init.sh b/src/.docker_modules/canu/1.6/docker_init.sh
new file mode 100755
index 00000000..0b96ce1e
--- /dev/null
+++ b/src/.docker_modules/canu/1.6/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/canu/1.6 -t 'lbmc/canu:1.6'
diff --git a/src/docker_modules/cutadapt/1.14/Dockerfile b/src/.docker_modules/cutadapt/1.14/Dockerfile
similarity index 100%
rename from src/docker_modules/cutadapt/1.14/Dockerfile
rename to src/.docker_modules/cutadapt/1.14/Dockerfile
diff --git a/src/.docker_modules/cutadapt/1.14/docker_init.sh b/src/.docker_modules/cutadapt/1.14/docker_init.sh
new file mode 100755
index 00000000..7390c9f6
--- /dev/null
+++ b/src/.docker_modules/cutadapt/1.14/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/cutadapt/1.14 -t 'lbmc/cutadapt:1.14'
diff --git a/src/docker_modules/cutadapt/1.15/Dockerfile b/src/.docker_modules/cutadapt/1.15/Dockerfile
similarity index 100%
rename from src/docker_modules/cutadapt/1.15/Dockerfile
rename to src/.docker_modules/cutadapt/1.15/Dockerfile
diff --git a/src/.docker_modules/cutadapt/1.15/docker_init.sh b/src/.docker_modules/cutadapt/1.15/docker_init.sh
new file mode 100755
index 00000000..c5ead618
--- /dev/null
+++ b/src/.docker_modules/cutadapt/1.15/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/cutadapt/1.15 -t 'lbmc/cutadapt:1.15'
diff --git a/src/docker_modules/cutadapt/2.1/Dockerfile b/src/.docker_modules/cutadapt/2.1/Dockerfile
similarity index 100%
rename from src/docker_modules/cutadapt/2.1/Dockerfile
rename to src/.docker_modules/cutadapt/2.1/Dockerfile
diff --git a/src/.docker_modules/cutadapt/2.1/docker_init.sh b/src/.docker_modules/cutadapt/2.1/docker_init.sh
new file mode 100755
index 00000000..4b55d68e
--- /dev/null
+++ b/src/.docker_modules/cutadapt/2.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/cutadapt/2.1 -t 'lbmc/cutadapt:2.1'
diff --git a/src/docker_modules/deeptools/3.0.2/Dockerfile b/src/.docker_modules/deeptools/3.0.2/Dockerfile
similarity index 100%
rename from src/docker_modules/deeptools/3.0.2/Dockerfile
rename to src/.docker_modules/deeptools/3.0.2/Dockerfile
diff --git a/src/.docker_modules/deeptools/3.0.2/docker_init.sh b/src/.docker_modules/deeptools/3.0.2/docker_init.sh
new file mode 100755
index 00000000..cb392df1
--- /dev/null
+++ b/src/.docker_modules/deeptools/3.0.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/deeptools/3.0.2 -t 'lbmc/deeptools:3.0.2'
diff --git a/src/docker_modules/deeptools/3.1.1/Dockerfile b/src/.docker_modules/deeptools/3.1.1/Dockerfile
similarity index 100%
rename from src/docker_modules/deeptools/3.1.1/Dockerfile
rename to src/.docker_modules/deeptools/3.1.1/Dockerfile
diff --git a/src/.docker_modules/deeptools/3.1.1/docker_init.sh b/src/.docker_modules/deeptools/3.1.1/docker_init.sh
new file mode 100755
index 00000000..7f0e94ff
--- /dev/null
+++ b/src/.docker_modules/deeptools/3.1.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/deeptools/3.1.1 -t 'lbmc/deeptools:3.1.1'
diff --git a/src/.docker_modules/docker_push.sh b/src/.docker_modules/docker_push.sh
new file mode 100755
index 00000000..37616d0f
--- /dev/null
+++ b/src/.docker_modules/docker_push.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+fd "Dockerfile" src/docke_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker push lbmc/"$0)}'
diff --git a/src/.docker_modules/docker_update.sh b/src/.docker_modules/docker_update.sh
new file mode 100644
index 00000000..1ac40cba
--- /dev/null
+++ b/src/.docker_modules/docker_update.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+fd "Dockerfile" src/docke_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker tag "$0" lbmc/" $0)}'
diff --git a/src/docker_modules/fastp/0.19.7/Dockerfile b/src/.docker_modules/fastp/0.19.7/Dockerfile
similarity index 100%
rename from src/docker_modules/fastp/0.19.7/Dockerfile
rename to src/.docker_modules/fastp/0.19.7/Dockerfile
diff --git a/src/.docker_modules/fastp/0.19.7/docker_init.sh b/src/.docker_modules/fastp/0.19.7/docker_init.sh
new file mode 100755
index 00000000..51b72579
--- /dev/null
+++ b/src/.docker_modules/fastp/0.19.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/fastp/0.19.7 -t 'lbmc/fastp:0.19.7'
diff --git a/src/docker_modules/fastqc/0.11.5/Dockerfile b/src/.docker_modules/fastqc/0.11.5/Dockerfile
similarity index 100%
rename from src/docker_modules/fastqc/0.11.5/Dockerfile
rename to src/.docker_modules/fastqc/0.11.5/Dockerfile
diff --git a/src/.docker_modules/fastqc/0.11.5/docker_init.sh b/src/.docker_modules/fastqc/0.11.5/docker_init.sh
new file mode 100755
index 00000000..d42d456c
--- /dev/null
+++ b/src/.docker_modules/fastqc/0.11.5/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/fastqc/0.11.5 -t 'lbmc/fastqc:0.11.5'
diff --git a/src/docker_modules/file_handle/0.1.1/Dockerfile b/src/.docker_modules/file_handle/0.1.1/Dockerfile
similarity index 100%
rename from src/docker_modules/file_handle/0.1.1/Dockerfile
rename to src/.docker_modules/file_handle/0.1.1/Dockerfile
diff --git a/src/.docker_modules/file_handle/0.1.1/docker_init.sh b/src/.docker_modules/file_handle/0.1.1/docker_init.sh
new file mode 100755
index 00000000..8fbeec24
--- /dev/null
+++ b/src/.docker_modules/file_handle/0.1.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/file_handle/0.1.1 -t 'lbmc/file_handle:0.1.1'
diff --git a/src/docker_modules/gatk/4.0.8.1/Dockerfile b/src/.docker_modules/gatk/4.0.8.1/Dockerfile
similarity index 100%
rename from src/docker_modules/gatk/4.0.8.1/Dockerfile
rename to src/.docker_modules/gatk/4.0.8.1/Dockerfile
diff --git a/src/.docker_modules/gatk/4.0.8.1/docker_init.sh b/src/.docker_modules/gatk/4.0.8.1/docker_init.sh
new file mode 100755
index 00000000..53631655
--- /dev/null
+++ b/src/.docker_modules/gatk/4.0.8.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/gatk/4.0.8.1 -t 'lbmc/gatk:4.0.8.1'
diff --git a/src/docker_modules/hisat2/2.0.0/Dockerfile b/src/.docker_modules/hisat2/2.0.0/Dockerfile
similarity index 100%
rename from src/docker_modules/hisat2/2.0.0/Dockerfile
rename to src/.docker_modules/hisat2/2.0.0/Dockerfile
diff --git a/src/.docker_modules/hisat2/2.0.0/docker_init.sh b/src/.docker_modules/hisat2/2.0.0/docker_init.sh
new file mode 100755
index 00000000..cff5d127
--- /dev/null
+++ b/src/.docker_modules/hisat2/2.0.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/hisat2/2.0.0 -t 'lbmc/hisat2:2.0.0'
diff --git a/src/docker_modules/hisat2/2.1.0/Dockerfile b/src/.docker_modules/hisat2/2.1.0/Dockerfile
similarity index 100%
rename from src/docker_modules/hisat2/2.1.0/Dockerfile
rename to src/.docker_modules/hisat2/2.1.0/Dockerfile
diff --git a/src/.docker_modules/hisat2/2.1.0/docker_init.sh b/src/.docker_modules/hisat2/2.1.0/docker_init.sh
new file mode 100755
index 00000000..bbae87ce
--- /dev/null
+++ b/src/.docker_modules/hisat2/2.1.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/hisat2/2.1.0 -t 'lbmc/hisat2:2.1.0'
diff --git a/src/docker_modules/htseq/0.11.2/Dockerfile b/src/.docker_modules/htseq/0.11.2/Dockerfile
similarity index 100%
rename from src/docker_modules/htseq/0.11.2/Dockerfile
rename to src/.docker_modules/htseq/0.11.2/Dockerfile
diff --git a/src/.docker_modules/htseq/0.11.2/docker_init.sh b/src/.docker_modules/htseq/0.11.2/docker_init.sh
new file mode 100755
index 00000000..f2ead722
--- /dev/null
+++ b/src/.docker_modules/htseq/0.11.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/htseq/0.11.2 -t 'lbmc/htseq:0.11.2'
diff --git a/src/docker_modules/htseq/0.8.0/Dockerfile b/src/.docker_modules/htseq/0.8.0/Dockerfile
similarity index 100%
rename from src/docker_modules/htseq/0.8.0/Dockerfile
rename to src/.docker_modules/htseq/0.8.0/Dockerfile
diff --git a/src/.docker_modules/htseq/0.8.0/docker_init.sh b/src/.docker_modules/htseq/0.8.0/docker_init.sh
new file mode 100755
index 00000000..09cf7277
--- /dev/null
+++ b/src/.docker_modules/htseq/0.8.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/htseq/0.8.0 -t 'lbmc/htseq:0.8.0'
diff --git a/src/docker_modules/kallisto/0.43.1/Dockerfile b/src/.docker_modules/kallisto/0.43.1/Dockerfile
similarity index 100%
rename from src/docker_modules/kallisto/0.43.1/Dockerfile
rename to src/.docker_modules/kallisto/0.43.1/Dockerfile
diff --git a/src/.docker_modules/kallisto/0.43.1/docker_init.sh b/src/.docker_modules/kallisto/0.43.1/docker_init.sh
new file mode 100755
index 00000000..1ff3aca3
--- /dev/null
+++ b/src/.docker_modules/kallisto/0.43.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/kallisto/0.43.1 -t 'lbmc/kallisto:0.43.1'
diff --git a/src/docker_modules/kallisto/0.44.0/Dockerfile b/src/.docker_modules/kallisto/0.44.0/Dockerfile
similarity index 100%
rename from src/docker_modules/kallisto/0.44.0/Dockerfile
rename to src/.docker_modules/kallisto/0.44.0/Dockerfile
diff --git a/src/.docker_modules/kallisto/0.44.0/docker_init.sh b/src/.docker_modules/kallisto/0.44.0/docker_init.sh
new file mode 100755
index 00000000..9e071b69
--- /dev/null
+++ b/src/.docker_modules/kallisto/0.44.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/kallisto/0.44.0 -t 'lbmc/kallisto:0.44.0'
diff --git a/src/docker_modules/macs2/2.1.2/Dockerfile b/src/.docker_modules/macs2/2.1.2/Dockerfile
similarity index 100%
rename from src/docker_modules/macs2/2.1.2/Dockerfile
rename to src/.docker_modules/macs2/2.1.2/Dockerfile
diff --git a/src/.docker_modules/macs2/2.1.2/docker_init.sh b/src/.docker_modules/macs2/2.1.2/docker_init.sh
new file mode 100755
index 00000000..02e9a382
--- /dev/null
+++ b/src/.docker_modules/macs2/2.1.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/macs2/2.1.2 -t 'lbmc/macs2:2.1.2'
diff --git a/src/docker_modules/multiqc/1.0/Dockerfile b/src/.docker_modules/multiqc/1.0/Dockerfile
similarity index 100%
rename from src/docker_modules/multiqc/1.0/Dockerfile
rename to src/.docker_modules/multiqc/1.0/Dockerfile
diff --git a/src/.docker_modules/multiqc/1.0/docker_init.sh b/src/.docker_modules/multiqc/1.0/docker_init.sh
new file mode 100755
index 00000000..0bab0761
--- /dev/null
+++ b/src/.docker_modules/multiqc/1.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/multiqc/1.0 -t 'lbmc/multiqc:1.0'
diff --git a/src/docker_modules/multiqc/1.7/Dockerfile b/src/.docker_modules/multiqc/1.7/Dockerfile
similarity index 100%
rename from src/docker_modules/multiqc/1.7/Dockerfile
rename to src/.docker_modules/multiqc/1.7/Dockerfile
diff --git a/src/.docker_modules/multiqc/1.7/docker_init.sh b/src/.docker_modules/multiqc/1.7/docker_init.sh
new file mode 100755
index 00000000..fb08cc12
--- /dev/null
+++ b/src/.docker_modules/multiqc/1.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/multiqc/1.7 -t 'lbmc/multiqc:1.7'
diff --git a/src/docker_modules/music/6613c53/Dockerfile b/src/.docker_modules/music/6613c53/Dockerfile
similarity index 100%
rename from src/docker_modules/music/6613c53/Dockerfile
rename to src/.docker_modules/music/6613c53/Dockerfile
diff --git a/src/.docker_modules/music/6613c53/docker_init.sh b/src/.docker_modules/music/6613c53/docker_init.sh
new file mode 100755
index 00000000..3666dfaa
--- /dev/null
+++ b/src/.docker_modules/music/6613c53/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/music/6613c53 -t 'lbmc/music:6613c53'
diff --git a/src/docker_modules/picard/2.18.11/Dockerfile b/src/.docker_modules/picard/2.18.11/Dockerfile
similarity index 100%
rename from src/docker_modules/picard/2.18.11/Dockerfile
rename to src/.docker_modules/picard/2.18.11/Dockerfile
diff --git a/src/docker_modules/picard/2.18.11/PicardCommandLine b/src/.docker_modules/picard/2.18.11/PicardCommandLine
similarity index 100%
rename from src/docker_modules/picard/2.18.11/PicardCommandLine
rename to src/.docker_modules/picard/2.18.11/PicardCommandLine
diff --git a/src/.docker_modules/picard/2.18.11/docker_init.sh b/src/.docker_modules/picard/2.18.11/docker_init.sh
new file mode 100755
index 00000000..3dc15851
--- /dev/null
+++ b/src/.docker_modules/picard/2.18.11/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/picard/2.18.11 -t 'lbmc/picard:2.18.11'
diff --git a/src/docker_modules/pigz/2.4/Dockerfile b/src/.docker_modules/pigz/2.4/Dockerfile
similarity index 100%
rename from src/docker_modules/pigz/2.4/Dockerfile
rename to src/.docker_modules/pigz/2.4/Dockerfile
diff --git a/src/.docker_modules/pigz/2.4/docker_init.sh b/src/.docker_modules/pigz/2.4/docker_init.sh
new file mode 100755
index 00000000..84e508a4
--- /dev/null
+++ b/src/.docker_modules/pigz/2.4/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/pigz/2.4 -t 'lbmc/pigz:2.4'
diff --git a/src/docker_modules/python/3.8/Dockerfile b/src/.docker_modules/python/3.8/Dockerfile
similarity index 100%
rename from src/docker_modules/python/3.8/Dockerfile
rename to src/.docker_modules/python/3.8/Dockerfile
diff --git a/src/.docker_modules/python/3.8/docker_init.sh b/src/.docker_modules/python/3.8/docker_init.sh
new file mode 100755
index 00000000..18b86e72
--- /dev/null
+++ b/src/.docker_modules/python/3.8/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/python/3.8 -t 'lbmc/python:3.8'
diff --git a/src/docker_modules/r/3.5.3/Dockerfile b/src/.docker_modules/r/3.5.3/Dockerfile
similarity index 100%
rename from src/docker_modules/r/3.5.3/Dockerfile
rename to src/.docker_modules/r/3.5.3/Dockerfile
diff --git a/src/.docker_modules/r/3.5.3/docker_init.sh b/src/.docker_modules/r/3.5.3/docker_init.sh
new file mode 100755
index 00000000..e9cb205e
--- /dev/null
+++ b/src/.docker_modules/r/3.5.3/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/r/3.5.3 -t 'lbmc/r:3.5.3'
diff --git a/src/docker_modules/rsem/1.3.0/Dockerfile b/src/.docker_modules/rsem/1.3.0/Dockerfile
similarity index 100%
rename from src/docker_modules/rsem/1.3.0/Dockerfile
rename to src/.docker_modules/rsem/1.3.0/Dockerfile
diff --git a/src/.docker_modules/rsem/1.3.0/docker_init.sh b/src/.docker_modules/rsem/1.3.0/docker_init.sh
new file mode 100755
index 00000000..2907c0ea
--- /dev/null
+++ b/src/.docker_modules/rsem/1.3.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/rsem/1.3.0 -t 'lbmc/rsem:1.3.0'
diff --git a/src/docker_modules/salmon/0.8.2/Dockerfile b/src/.docker_modules/salmon/0.8.2/Dockerfile
similarity index 100%
rename from src/docker_modules/salmon/0.8.2/Dockerfile
rename to src/.docker_modules/salmon/0.8.2/Dockerfile
diff --git a/src/.docker_modules/salmon/0.8.2/docker_init.sh b/src/.docker_modules/salmon/0.8.2/docker_init.sh
new file mode 100755
index 00000000..3a776c08
--- /dev/null
+++ b/src/.docker_modules/salmon/0.8.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/salmon/0.8.2 -t 'lbmc/salmon:0.8.2'
diff --git a/src/docker_modules/sambamba/0.6.7/Dockerfile b/src/.docker_modules/sambamba/0.6.7/Dockerfile
similarity index 100%
rename from src/docker_modules/sambamba/0.6.7/Dockerfile
rename to src/.docker_modules/sambamba/0.6.7/Dockerfile
diff --git a/src/.docker_modules/sambamba/0.6.7/docker_init.sh b/src/.docker_modules/sambamba/0.6.7/docker_init.sh
new file mode 100755
index 00000000..d203b20c
--- /dev/null
+++ b/src/.docker_modules/sambamba/0.6.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/sambamba/0.6.7 -t 'lbmc/sambamba:0.6.7'
diff --git a/src/docker_modules/sambamba/0.6.9/Dockerfile b/src/.docker_modules/sambamba/0.6.9/Dockerfile
similarity index 100%
rename from src/docker_modules/sambamba/0.6.9/Dockerfile
rename to src/.docker_modules/sambamba/0.6.9/Dockerfile
diff --git a/src/.docker_modules/sambamba/0.6.9/docker_init.sh b/src/.docker_modules/sambamba/0.6.9/docker_init.sh
new file mode 100755
index 00000000..7431118e
--- /dev/null
+++ b/src/.docker_modules/sambamba/0.6.9/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/sambamba/0.6.9 -t 'lbmc/sambamba:0.6.9'
diff --git a/src/docker_modules/samblaster/0.1.24/Dockerfile b/src/.docker_modules/samblaster/0.1.24/Dockerfile
similarity index 100%
rename from src/docker_modules/samblaster/0.1.24/Dockerfile
rename to src/.docker_modules/samblaster/0.1.24/Dockerfile
diff --git a/src/.docker_modules/samblaster/0.1.24/docker_init.sh b/src/.docker_modules/samblaster/0.1.24/docker_init.sh
new file mode 100755
index 00000000..991b92cb
--- /dev/null
+++ b/src/.docker_modules/samblaster/0.1.24/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/samblaster/0.1.24 -t 'lbmc/samblaster:0.1.24'
diff --git a/src/docker_modules/samtools/1.7/Dockerfile b/src/.docker_modules/samtools/1.7/Dockerfile
similarity index 100%
rename from src/docker_modules/samtools/1.7/Dockerfile
rename to src/.docker_modules/samtools/1.7/Dockerfile
diff --git a/src/.docker_modules/samtools/1.7/docker_init.sh b/src/.docker_modules/samtools/1.7/docker_init.sh
new file mode 100755
index 00000000..4c47e22b
--- /dev/null
+++ b/src/.docker_modules/samtools/1.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/samtools/1.7 -t 'lbmc/samtools:1.7'
diff --git a/src/docker_modules/sratoolkit/2.8.2/Dockerfile b/src/.docker_modules/sratoolkit/2.8.2/Dockerfile
similarity index 100%
rename from src/docker_modules/sratoolkit/2.8.2/Dockerfile
rename to src/.docker_modules/sratoolkit/2.8.2/Dockerfile
diff --git a/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh b/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
new file mode 100755
index 00000000..a7f547e1
--- /dev/null
+++ b/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/sratoolkit/2.8.2 -t 'lbmc/sratoolkit:2.8.2'
diff --git a/src/docker_modules/subread/1.6.4/Dockerfile b/src/.docker_modules/subread/1.6.4/Dockerfile
similarity index 100%
rename from src/docker_modules/subread/1.6.4/Dockerfile
rename to src/.docker_modules/subread/1.6.4/Dockerfile
diff --git a/src/.docker_modules/subread/1.6.4/docker_init.sh b/src/.docker_modules/subread/1.6.4/docker_init.sh
new file mode 100755
index 00000000..574c2031
--- /dev/null
+++ b/src/.docker_modules/subread/1.6.4/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/subread/1.6.4 -t 'lbmc/subread:1.6.4'
diff --git a/src/docker_modules/tophat/2.1.1/Dockerfile b/src/.docker_modules/tophat/2.1.1/Dockerfile
similarity index 100%
rename from src/docker_modules/tophat/2.1.1/Dockerfile
rename to src/.docker_modules/tophat/2.1.1/Dockerfile
diff --git a/src/.docker_modules/tophat/2.1.1/docker_init.sh b/src/.docker_modules/tophat/2.1.1/docker_init.sh
new file mode 100755
index 00000000..a6125a86
--- /dev/null
+++ b/src/.docker_modules/tophat/2.1.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/tophat/2.1.1 -t 'lbmc/tophat:2.1.1'
diff --git a/src/docker_modules/trimmomatic/0.36/Dockerfile b/src/.docker_modules/trimmomatic/0.36/Dockerfile
similarity index 100%
rename from src/docker_modules/trimmomatic/0.36/Dockerfile
rename to src/.docker_modules/trimmomatic/0.36/Dockerfile
diff --git a/src/.docker_modules/trimmomatic/0.36/docker_init.sh b/src/.docker_modules/trimmomatic/0.36/docker_init.sh
new file mode 100755
index 00000000..27c970f4
--- /dev/null
+++ b/src/.docker_modules/trimmomatic/0.36/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/trimmomatic/0.36 -t 'lbmc/trimmomatic:0.36'
diff --git a/src/docker_modules/ucsc/375/Dockerfile b/src/.docker_modules/ucsc/375/Dockerfile
similarity index 100%
rename from src/docker_modules/ucsc/375/Dockerfile
rename to src/.docker_modules/ucsc/375/Dockerfile
diff --git a/src/.docker_modules/ucsc/375/docker_init.sh b/src/.docker_modules/ucsc/375/docker_init.sh
new file mode 100755
index 00000000..5fd1371c
--- /dev/null
+++ b/src/.docker_modules/ucsc/375/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/ucsc/375/ -t 'lbmc/ucsc:375'
diff --git a/src/docker_modules/umi_tools/0.5.4/Dockerfile b/src/.docker_modules/umi_tools/0.5.4/Dockerfile
similarity index 100%
rename from src/docker_modules/umi_tools/0.5.4/Dockerfile
rename to src/.docker_modules/umi_tools/0.5.4/Dockerfile
diff --git a/src/.docker_modules/umi_tools/0.5.4/docker_init.sh b/src/.docker_modules/umi_tools/0.5.4/docker_init.sh
new file mode 100755
index 00000000..1b11e25d
--- /dev/null
+++ b/src/.docker_modules/umi_tools/0.5.4/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
diff --git a/src/docker_modules/umi_tools/1.0.0/Dockerfile b/src/.docker_modules/umi_tools/1.0.0/Dockerfile
similarity index 100%
rename from src/docker_modules/umi_tools/1.0.0/Dockerfile
rename to src/.docker_modules/umi_tools/1.0.0/Dockerfile
diff --git a/src/.docker_modules/umi_tools/1.0.0/docker_init.sh b/src/.docker_modules/umi_tools/1.0.0/docker_init.sh
new file mode 100755
index 00000000..1b11e25d
--- /dev/null
+++ b/src/.docker_modules/umi_tools/1.0.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
diff --git a/src/docker_modules/urqt/d62c1f8/Dockerfile b/src/.docker_modules/urqt/d62c1f8/Dockerfile
similarity index 100%
rename from src/docker_modules/urqt/d62c1f8/Dockerfile
rename to src/.docker_modules/urqt/d62c1f8/Dockerfile
diff --git a/src/.docker_modules/urqt/d62c1f8/docker_init.sh b/src/.docker_modules/urqt/d62c1f8/docker_init.sh
new file mode 100755
index 00000000..bb7f161f
--- /dev/null
+++ b/src/.docker_modules/urqt/d62c1f8/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/urqt/d62c1f8 -t 'lbmc/urqt:d62c1f8'
diff --git a/src/singularity_modules/bcftools/1.7/bcftools b/src/.singularity_modules/bcftools/1.7/bcftools
similarity index 100%
rename from src/singularity_modules/bcftools/1.7/bcftools
rename to src/.singularity_modules/bcftools/1.7/bcftools
diff --git a/src/singularity_modules/bcftools/1.7/bcftools.def b/src/.singularity_modules/bcftools/1.7/bcftools.def
similarity index 100%
rename from src/singularity_modules/bcftools/1.7/bcftools.def
rename to src/.singularity_modules/bcftools/1.7/bcftools.def
diff --git a/src/singularity_modules/bcftools/1.7/build.sh b/src/.singularity_modules/bcftools/1.7/build.sh
similarity index 100%
rename from src/singularity_modules/bcftools/1.7/build.sh
rename to src/.singularity_modules/bcftools/1.7/build.sh
diff --git a/src/singularity_modules/bedtools/2.25.0/bedtools b/src/.singularity_modules/bedtools/2.25.0/bedtools
similarity index 100%
rename from src/singularity_modules/bedtools/2.25.0/bedtools
rename to src/.singularity_modules/bedtools/2.25.0/bedtools
diff --git a/src/singularity_modules/bedtools/2.25.0/bedtools.def b/src/.singularity_modules/bedtools/2.25.0/bedtools.def
similarity index 100%
rename from src/singularity_modules/bedtools/2.25.0/bedtools.def
rename to src/.singularity_modules/bedtools/2.25.0/bedtools.def
diff --git a/src/singularity_modules/bedtools/2.25.0/build.sh b/src/.singularity_modules/bedtools/2.25.0/build.sh
similarity index 100%
rename from src/singularity_modules/bedtools/2.25.0/build.sh
rename to src/.singularity_modules/bedtools/2.25.0/build.sh
diff --git a/src/singularity_modules/bioawk/1.0/bioawk b/src/.singularity_modules/bioawk/1.0/bioawk
similarity index 100%
rename from src/singularity_modules/bioawk/1.0/bioawk
rename to src/.singularity_modules/bioawk/1.0/bioawk
diff --git a/src/singularity_modules/bioawk/1.0/bioawk.def b/src/.singularity_modules/bioawk/1.0/bioawk.def
similarity index 100%
rename from src/singularity_modules/bioawk/1.0/bioawk.def
rename to src/.singularity_modules/bioawk/1.0/bioawk.def
diff --git a/src/singularity_modules/bioawk/1.0/build.sh b/src/.singularity_modules/bioawk/1.0/build.sh
similarity index 100%
rename from src/singularity_modules/bioawk/1.0/build.sh
rename to src/.singularity_modules/bioawk/1.0/build.sh
diff --git a/src/singularity_modules/bowtie/1.2.2/bowtie b/src/.singularity_modules/bowtie/1.2.2/bowtie
similarity index 100%
rename from src/singularity_modules/bowtie/1.2.2/bowtie
rename to src/.singularity_modules/bowtie/1.2.2/bowtie
diff --git a/src/singularity_modules/bowtie/1.2.2/bowtie.def b/src/.singularity_modules/bowtie/1.2.2/bowtie.def
similarity index 100%
rename from src/singularity_modules/bowtie/1.2.2/bowtie.def
rename to src/.singularity_modules/bowtie/1.2.2/bowtie.def
diff --git a/src/singularity_modules/bowtie/1.2.2/build.sh b/src/.singularity_modules/bowtie/1.2.2/build.sh
similarity index 100%
rename from src/singularity_modules/bowtie/1.2.2/build.sh
rename to src/.singularity_modules/bowtie/1.2.2/build.sh
diff --git a/src/singularity_modules/bowtie2/2.3.4.1/bowtie2 b/src/.singularity_modules/bowtie2/2.3.4.1/bowtie2
similarity index 100%
rename from src/singularity_modules/bowtie2/2.3.4.1/bowtie2
rename to src/.singularity_modules/bowtie2/2.3.4.1/bowtie2
diff --git a/src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def b/src/.singularity_modules/bowtie2/2.3.4.1/bowtie2.def
similarity index 100%
rename from src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def
rename to src/.singularity_modules/bowtie2/2.3.4.1/bowtie2.def
diff --git a/src/singularity_modules/bowtie2/2.3.4.1/build.sh b/src/.singularity_modules/bowtie2/2.3.4.1/build.sh
similarity index 100%
rename from src/singularity_modules/bowtie2/2.3.4.1/build.sh
rename to src/.singularity_modules/bowtie2/2.3.4.1/build.sh
diff --git a/src/singularity_modules/bwa/0.7.17/build.sh b/src/.singularity_modules/bwa/0.7.17/build.sh
similarity index 100%
rename from src/singularity_modules/bwa/0.7.17/build.sh
rename to src/.singularity_modules/bwa/0.7.17/build.sh
diff --git a/src/singularity_modules/bwa/0.7.17/bwa b/src/.singularity_modules/bwa/0.7.17/bwa
similarity index 100%
rename from src/singularity_modules/bwa/0.7.17/bwa
rename to src/.singularity_modules/bwa/0.7.17/bwa
diff --git a/src/singularity_modules/bwa/0.7.17/bwa.def b/src/.singularity_modules/bwa/0.7.17/bwa.def
similarity index 100%
rename from src/singularity_modules/bwa/0.7.17/bwa.def
rename to src/.singularity_modules/bwa/0.7.17/bwa.def
diff --git a/src/singularity_modules/canu/1.6/build.sh b/src/.singularity_modules/canu/1.6/build.sh
similarity index 100%
rename from src/singularity_modules/canu/1.6/build.sh
rename to src/.singularity_modules/canu/1.6/build.sh
diff --git a/src/singularity_modules/canu/1.6/canu b/src/.singularity_modules/canu/1.6/canu
similarity index 100%
rename from src/singularity_modules/canu/1.6/canu
rename to src/.singularity_modules/canu/1.6/canu
diff --git a/src/singularity_modules/canu/1.6/canu.def b/src/.singularity_modules/canu/1.6/canu.def
similarity index 100%
rename from src/singularity_modules/canu/1.6/canu.def
rename to src/.singularity_modules/canu/1.6/canu.def
diff --git a/src/singularity_modules/cutadapt/1.14/build.sh b/src/.singularity_modules/cutadapt/1.14/build.sh
similarity index 100%
rename from src/singularity_modules/cutadapt/1.14/build.sh
rename to src/.singularity_modules/cutadapt/1.14/build.sh
diff --git a/src/singularity_modules/cutadapt/1.14/cutadapt b/src/.singularity_modules/cutadapt/1.14/cutadapt
similarity index 100%
rename from src/singularity_modules/cutadapt/1.14/cutadapt
rename to src/.singularity_modules/cutadapt/1.14/cutadapt
diff --git a/src/singularity_modules/cutadapt/1.14/cutadapt.def b/src/.singularity_modules/cutadapt/1.14/cutadapt.def
similarity index 100%
rename from src/singularity_modules/cutadapt/1.14/cutadapt.def
rename to src/.singularity_modules/cutadapt/1.14/cutadapt.def
diff --git a/src/singularity_modules/cutadapt/1.15/build.sh b/src/.singularity_modules/cutadapt/1.15/build.sh
similarity index 100%
rename from src/singularity_modules/cutadapt/1.15/build.sh
rename to src/.singularity_modules/cutadapt/1.15/build.sh
diff --git a/src/singularity_modules/cutadapt/1.15/cutadapt b/src/.singularity_modules/cutadapt/1.15/cutadapt
similarity index 100%
rename from src/singularity_modules/cutadapt/1.15/cutadapt
rename to src/.singularity_modules/cutadapt/1.15/cutadapt
diff --git a/src/singularity_modules/cutadapt/1.15/cutadapt.def b/src/.singularity_modules/cutadapt/1.15/cutadapt.def
similarity index 100%
rename from src/singularity_modules/cutadapt/1.15/cutadapt.def
rename to src/.singularity_modules/cutadapt/1.15/cutadapt.def
diff --git a/src/singularity_modules/cutadapt/2.1/build.sh b/src/.singularity_modules/cutadapt/2.1/build.sh
similarity index 100%
rename from src/singularity_modules/cutadapt/2.1/build.sh
rename to src/.singularity_modules/cutadapt/2.1/build.sh
diff --git a/src/singularity_modules/cutadapt/2.1/cutadapt b/src/.singularity_modules/cutadapt/2.1/cutadapt
similarity index 100%
rename from src/singularity_modules/cutadapt/2.1/cutadapt
rename to src/.singularity_modules/cutadapt/2.1/cutadapt
diff --git a/src/singularity_modules/cutadapt/2.1/cutadapt.def b/src/.singularity_modules/cutadapt/2.1/cutadapt.def
similarity index 100%
rename from src/singularity_modules/cutadapt/2.1/cutadapt.def
rename to src/.singularity_modules/cutadapt/2.1/cutadapt.def
diff --git a/src/singularity_modules/deeptools/3.0.2/build.sh b/src/.singularity_modules/deeptools/3.0.2/build.sh
similarity index 100%
rename from src/singularity_modules/deeptools/3.0.2/build.sh
rename to src/.singularity_modules/deeptools/3.0.2/build.sh
diff --git a/src/singularity_modules/deeptools/3.0.2/deeptools b/src/.singularity_modules/deeptools/3.0.2/deeptools
similarity index 100%
rename from src/singularity_modules/deeptools/3.0.2/deeptools
rename to src/.singularity_modules/deeptools/3.0.2/deeptools
diff --git a/src/singularity_modules/deeptools/3.0.2/deeptools.def b/src/.singularity_modules/deeptools/3.0.2/deeptools.def
similarity index 100%
rename from src/singularity_modules/deeptools/3.0.2/deeptools.def
rename to src/.singularity_modules/deeptools/3.0.2/deeptools.def
diff --git a/src/singularity_modules/deeptools/3.1.1/build.sh b/src/.singularity_modules/deeptools/3.1.1/build.sh
similarity index 100%
rename from src/singularity_modules/deeptools/3.1.1/build.sh
rename to src/.singularity_modules/deeptools/3.1.1/build.sh
diff --git a/src/singularity_modules/deeptools/3.1.1/deeptools b/src/.singularity_modules/deeptools/3.1.1/deeptools
similarity index 100%
rename from src/singularity_modules/deeptools/3.1.1/deeptools
rename to src/.singularity_modules/deeptools/3.1.1/deeptools
diff --git a/src/singularity_modules/deeptools/3.1.1/deeptools.def b/src/.singularity_modules/deeptools/3.1.1/deeptools.def
similarity index 100%
rename from src/singularity_modules/deeptools/3.1.1/deeptools.def
rename to src/.singularity_modules/deeptools/3.1.1/deeptools.def
diff --git a/src/singularity_modules/docker_to_singularity.sh b/src/.singularity_modules/docker_to_singularity.sh
similarity index 100%
rename from src/singularity_modules/docker_to_singularity.sh
rename to src/.singularity_modules/docker_to_singularity.sh
diff --git a/src/singularity_modules/fastp/0.19.7/build.sh b/src/.singularity_modules/fastp/0.19.7/build.sh
similarity index 100%
rename from src/singularity_modules/fastp/0.19.7/build.sh
rename to src/.singularity_modules/fastp/0.19.7/build.sh
diff --git a/src/singularity_modules/fastp/0.19.7/fastp b/src/.singularity_modules/fastp/0.19.7/fastp
similarity index 100%
rename from src/singularity_modules/fastp/0.19.7/fastp
rename to src/.singularity_modules/fastp/0.19.7/fastp
diff --git a/src/singularity_modules/fastp/0.19.7/fastp.def b/src/.singularity_modules/fastp/0.19.7/fastp.def
similarity index 100%
rename from src/singularity_modules/fastp/0.19.7/fastp.def
rename to src/.singularity_modules/fastp/0.19.7/fastp.def
diff --git a/src/singularity_modules/fastqc/0.11.5/build.sh b/src/.singularity_modules/fastqc/0.11.5/build.sh
similarity index 100%
rename from src/singularity_modules/fastqc/0.11.5/build.sh
rename to src/.singularity_modules/fastqc/0.11.5/build.sh
diff --git a/src/singularity_modules/fastqc/0.11.5/fastqc b/src/.singularity_modules/fastqc/0.11.5/fastqc
similarity index 100%
rename from src/singularity_modules/fastqc/0.11.5/fastqc
rename to src/.singularity_modules/fastqc/0.11.5/fastqc
diff --git a/src/singularity_modules/fastqc/0.11.5/fastqc.def b/src/.singularity_modules/fastqc/0.11.5/fastqc.def
similarity index 100%
rename from src/singularity_modules/fastqc/0.11.5/fastqc.def
rename to src/.singularity_modules/fastqc/0.11.5/fastqc.def
diff --git a/src/singularity_modules/file_handle/0.1.1/build.sh b/src/.singularity_modules/file_handle/0.1.1/build.sh
similarity index 100%
rename from src/singularity_modules/file_handle/0.1.1/build.sh
rename to src/.singularity_modules/file_handle/0.1.1/build.sh
diff --git a/src/singularity_modules/file_handle/0.1.1/file_handle b/src/.singularity_modules/file_handle/0.1.1/file_handle
similarity index 100%
rename from src/singularity_modules/file_handle/0.1.1/file_handle
rename to src/.singularity_modules/file_handle/0.1.1/file_handle
diff --git a/src/singularity_modules/file_handle/0.1.1/file_handle.def b/src/.singularity_modules/file_handle/0.1.1/file_handle.def
similarity index 100%
rename from src/singularity_modules/file_handle/0.1.1/file_handle.def
rename to src/.singularity_modules/file_handle/0.1.1/file_handle.def
diff --git a/src/singularity_modules/gatk/4.0.8.1/build.sh b/src/.singularity_modules/gatk/4.0.8.1/build.sh
similarity index 100%
rename from src/singularity_modules/gatk/4.0.8.1/build.sh
rename to src/.singularity_modules/gatk/4.0.8.1/build.sh
diff --git a/src/singularity_modules/gatk/4.0.8.1/gatk b/src/.singularity_modules/gatk/4.0.8.1/gatk
similarity index 100%
rename from src/singularity_modules/gatk/4.0.8.1/gatk
rename to src/.singularity_modules/gatk/4.0.8.1/gatk
diff --git a/src/singularity_modules/gatk/4.0.8.1/gatk.def b/src/.singularity_modules/gatk/4.0.8.1/gatk.def
similarity index 100%
rename from src/singularity_modules/gatk/4.0.8.1/gatk.def
rename to src/.singularity_modules/gatk/4.0.8.1/gatk.def
diff --git a/src/singularity_modules/hisat2/2.0.0/build.sh b/src/.singularity_modules/hisat2/2.0.0/build.sh
similarity index 100%
rename from src/singularity_modules/hisat2/2.0.0/build.sh
rename to src/.singularity_modules/hisat2/2.0.0/build.sh
diff --git a/src/singularity_modules/hisat2/2.0.0/hisat2 b/src/.singularity_modules/hisat2/2.0.0/hisat2
similarity index 100%
rename from src/singularity_modules/hisat2/2.0.0/hisat2
rename to src/.singularity_modules/hisat2/2.0.0/hisat2
diff --git a/src/singularity_modules/hisat2/2.0.0/hisat2.def b/src/.singularity_modules/hisat2/2.0.0/hisat2.def
similarity index 100%
rename from src/singularity_modules/hisat2/2.0.0/hisat2.def
rename to src/.singularity_modules/hisat2/2.0.0/hisat2.def
diff --git a/src/singularity_modules/hisat2/2.1.0/build.sh b/src/.singularity_modules/hisat2/2.1.0/build.sh
similarity index 100%
rename from src/singularity_modules/hisat2/2.1.0/build.sh
rename to src/.singularity_modules/hisat2/2.1.0/build.sh
diff --git a/src/singularity_modules/hisat2/2.1.0/hisat2 b/src/.singularity_modules/hisat2/2.1.0/hisat2
similarity index 100%
rename from src/singularity_modules/hisat2/2.1.0/hisat2
rename to src/.singularity_modules/hisat2/2.1.0/hisat2
diff --git a/src/singularity_modules/hisat2/2.1.0/hisat2.def b/src/.singularity_modules/hisat2/2.1.0/hisat2.def
similarity index 100%
rename from src/singularity_modules/hisat2/2.1.0/hisat2.def
rename to src/.singularity_modules/hisat2/2.1.0/hisat2.def
diff --git a/src/singularity_modules/htseq/0.11.2/build.sh b/src/.singularity_modules/htseq/0.11.2/build.sh
similarity index 100%
rename from src/singularity_modules/htseq/0.11.2/build.sh
rename to src/.singularity_modules/htseq/0.11.2/build.sh
diff --git a/src/singularity_modules/htseq/0.11.2/htseq b/src/.singularity_modules/htseq/0.11.2/htseq
similarity index 100%
rename from src/singularity_modules/htseq/0.11.2/htseq
rename to src/.singularity_modules/htseq/0.11.2/htseq
diff --git a/src/singularity_modules/htseq/0.11.2/htseq.def b/src/.singularity_modules/htseq/0.11.2/htseq.def
similarity index 100%
rename from src/singularity_modules/htseq/0.11.2/htseq.def
rename to src/.singularity_modules/htseq/0.11.2/htseq.def
diff --git a/src/singularity_modules/htseq/0.8.0/build.sh b/src/.singularity_modules/htseq/0.8.0/build.sh
similarity index 100%
rename from src/singularity_modules/htseq/0.8.0/build.sh
rename to src/.singularity_modules/htseq/0.8.0/build.sh
diff --git a/src/singularity_modules/htseq/0.8.0/htseq b/src/.singularity_modules/htseq/0.8.0/htseq
similarity index 100%
rename from src/singularity_modules/htseq/0.8.0/htseq
rename to src/.singularity_modules/htseq/0.8.0/htseq
diff --git a/src/singularity_modules/htseq/0.8.0/htseq.def b/src/.singularity_modules/htseq/0.8.0/htseq.def
similarity index 100%
rename from src/singularity_modules/htseq/0.8.0/htseq.def
rename to src/.singularity_modules/htseq/0.8.0/htseq.def
diff --git a/src/singularity_modules/kallisto/0.43.1/build.sh b/src/.singularity_modules/kallisto/0.43.1/build.sh
similarity index 100%
rename from src/singularity_modules/kallisto/0.43.1/build.sh
rename to src/.singularity_modules/kallisto/0.43.1/build.sh
diff --git a/src/singularity_modules/kallisto/0.43.1/kallisto b/src/.singularity_modules/kallisto/0.43.1/kallisto
similarity index 100%
rename from src/singularity_modules/kallisto/0.43.1/kallisto
rename to src/.singularity_modules/kallisto/0.43.1/kallisto
diff --git a/src/singularity_modules/kallisto/0.43.1/kallisto.def b/src/.singularity_modules/kallisto/0.43.1/kallisto.def
similarity index 100%
rename from src/singularity_modules/kallisto/0.43.1/kallisto.def
rename to src/.singularity_modules/kallisto/0.43.1/kallisto.def
diff --git a/src/singularity_modules/kallisto/0.44.0/build.sh b/src/.singularity_modules/kallisto/0.44.0/build.sh
similarity index 100%
rename from src/singularity_modules/kallisto/0.44.0/build.sh
rename to src/.singularity_modules/kallisto/0.44.0/build.sh
diff --git a/src/singularity_modules/kallisto/0.44.0/kallisto b/src/.singularity_modules/kallisto/0.44.0/kallisto
similarity index 100%
rename from src/singularity_modules/kallisto/0.44.0/kallisto
rename to src/.singularity_modules/kallisto/0.44.0/kallisto
diff --git a/src/singularity_modules/kallisto/0.44.0/kallisto.def b/src/.singularity_modules/kallisto/0.44.0/kallisto.def
similarity index 100%
rename from src/singularity_modules/kallisto/0.44.0/kallisto.def
rename to src/.singularity_modules/kallisto/0.44.0/kallisto.def
diff --git a/src/singularity_modules/macs2/2.1.2/build.sh b/src/.singularity_modules/macs2/2.1.2/build.sh
similarity index 100%
rename from src/singularity_modules/macs2/2.1.2/build.sh
rename to src/.singularity_modules/macs2/2.1.2/build.sh
diff --git a/src/singularity_modules/macs2/2.1.2/macs2 b/src/.singularity_modules/macs2/2.1.2/macs2
similarity index 100%
rename from src/singularity_modules/macs2/2.1.2/macs2
rename to src/.singularity_modules/macs2/2.1.2/macs2
diff --git a/src/singularity_modules/macs2/2.1.2/macs2.def b/src/.singularity_modules/macs2/2.1.2/macs2.def
similarity index 100%
rename from src/singularity_modules/macs2/2.1.2/macs2.def
rename to src/.singularity_modules/macs2/2.1.2/macs2.def
diff --git a/src/singularity_modules/multiqc/1.0/build.sh b/src/.singularity_modules/multiqc/1.0/build.sh
similarity index 100%
rename from src/singularity_modules/multiqc/1.0/build.sh
rename to src/.singularity_modules/multiqc/1.0/build.sh
diff --git a/src/singularity_modules/multiqc/1.0/multiqc b/src/.singularity_modules/multiqc/1.0/multiqc
similarity index 100%
rename from src/singularity_modules/multiqc/1.0/multiqc
rename to src/.singularity_modules/multiqc/1.0/multiqc
diff --git a/src/singularity_modules/multiqc/1.0/multiqc.def b/src/.singularity_modules/multiqc/1.0/multiqc.def
similarity index 100%
rename from src/singularity_modules/multiqc/1.0/multiqc.def
rename to src/.singularity_modules/multiqc/1.0/multiqc.def
diff --git a/src/singularity_modules/multiqc/1.7/build.sh b/src/.singularity_modules/multiqc/1.7/build.sh
similarity index 100%
rename from src/singularity_modules/multiqc/1.7/build.sh
rename to src/.singularity_modules/multiqc/1.7/build.sh
diff --git a/src/singularity_modules/multiqc/1.7/multiqc b/src/.singularity_modules/multiqc/1.7/multiqc
similarity index 100%
rename from src/singularity_modules/multiqc/1.7/multiqc
rename to src/.singularity_modules/multiqc/1.7/multiqc
diff --git a/src/singularity_modules/multiqc/1.7/multiqc.def b/src/.singularity_modules/multiqc/1.7/multiqc.def
similarity index 100%
rename from src/singularity_modules/multiqc/1.7/multiqc.def
rename to src/.singularity_modules/multiqc/1.7/multiqc.def
diff --git a/src/singularity_modules/music/6613c53/build.sh b/src/.singularity_modules/music/6613c53/build.sh
similarity index 100%
rename from src/singularity_modules/music/6613c53/build.sh
rename to src/.singularity_modules/music/6613c53/build.sh
diff --git a/src/singularity_modules/music/6613c53/music b/src/.singularity_modules/music/6613c53/music
similarity index 100%
rename from src/singularity_modules/music/6613c53/music
rename to src/.singularity_modules/music/6613c53/music
diff --git a/src/singularity_modules/music/6613c53/music.def b/src/.singularity_modules/music/6613c53/music.def
similarity index 100%
rename from src/singularity_modules/music/6613c53/music.def
rename to src/.singularity_modules/music/6613c53/music.def
diff --git a/src/singularity_modules/picard/2.18.11/PicardCommandLine b/src/.singularity_modules/picard/2.18.11/PicardCommandLine
similarity index 100%
rename from src/singularity_modules/picard/2.18.11/PicardCommandLine
rename to src/.singularity_modules/picard/2.18.11/PicardCommandLine
diff --git a/src/singularity_modules/picard/2.18.11/build.sh b/src/.singularity_modules/picard/2.18.11/build.sh
similarity index 100%
rename from src/singularity_modules/picard/2.18.11/build.sh
rename to src/.singularity_modules/picard/2.18.11/build.sh
diff --git a/src/singularity_modules/picard/2.18.11/picard b/src/.singularity_modules/picard/2.18.11/picard
similarity index 100%
rename from src/singularity_modules/picard/2.18.11/picard
rename to src/.singularity_modules/picard/2.18.11/picard
diff --git a/src/singularity_modules/picard/2.18.11/picard.def b/src/.singularity_modules/picard/2.18.11/picard.def
similarity index 100%
rename from src/singularity_modules/picard/2.18.11/picard.def
rename to src/.singularity_modules/picard/2.18.11/picard.def
diff --git a/src/singularity_modules/pigz/2.4/build.sh b/src/.singularity_modules/pigz/2.4/build.sh
similarity index 100%
rename from src/singularity_modules/pigz/2.4/build.sh
rename to src/.singularity_modules/pigz/2.4/build.sh
diff --git a/src/singularity_modules/pigz/2.4/pigz b/src/.singularity_modules/pigz/2.4/pigz
similarity index 100%
rename from src/singularity_modules/pigz/2.4/pigz
rename to src/.singularity_modules/pigz/2.4/pigz
diff --git a/src/singularity_modules/pigz/2.4/pigz.def b/src/.singularity_modules/pigz/2.4/pigz.def
similarity index 100%
rename from src/singularity_modules/pigz/2.4/pigz.def
rename to src/.singularity_modules/pigz/2.4/pigz.def
diff --git a/src/singularity_modules/r/3.5.3/build.sh b/src/.singularity_modules/r/3.5.3/build.sh
similarity index 100%
rename from src/singularity_modules/r/3.5.3/build.sh
rename to src/.singularity_modules/r/3.5.3/build.sh
diff --git a/src/singularity_modules/r/3.5.3/r b/src/.singularity_modules/r/3.5.3/r
similarity index 100%
rename from src/singularity_modules/r/3.5.3/r
rename to src/.singularity_modules/r/3.5.3/r
diff --git a/src/singularity_modules/r/3.5.3/r.def b/src/.singularity_modules/r/3.5.3/r.def
similarity index 100%
rename from src/singularity_modules/r/3.5.3/r.def
rename to src/.singularity_modules/r/3.5.3/r.def
diff --git a/src/singularity_modules/rsem/1.3.0/build.sh b/src/.singularity_modules/rsem/1.3.0/build.sh
similarity index 100%
rename from src/singularity_modules/rsem/1.3.0/build.sh
rename to src/.singularity_modules/rsem/1.3.0/build.sh
diff --git a/src/singularity_modules/rsem/1.3.0/rsem b/src/.singularity_modules/rsem/1.3.0/rsem
similarity index 100%
rename from src/singularity_modules/rsem/1.3.0/rsem
rename to src/.singularity_modules/rsem/1.3.0/rsem
diff --git a/src/singularity_modules/rsem/1.3.0/rsem.def b/src/.singularity_modules/rsem/1.3.0/rsem.def
similarity index 100%
rename from src/singularity_modules/rsem/1.3.0/rsem.def
rename to src/.singularity_modules/rsem/1.3.0/rsem.def
diff --git a/src/singularity_modules/salmon/0.8.2/build.sh b/src/.singularity_modules/salmon/0.8.2/build.sh
similarity index 100%
rename from src/singularity_modules/salmon/0.8.2/build.sh
rename to src/.singularity_modules/salmon/0.8.2/build.sh
diff --git a/src/singularity_modules/salmon/0.8.2/salmon b/src/.singularity_modules/salmon/0.8.2/salmon
similarity index 100%
rename from src/singularity_modules/salmon/0.8.2/salmon
rename to src/.singularity_modules/salmon/0.8.2/salmon
diff --git a/src/singularity_modules/salmon/0.8.2/salmon.def b/src/.singularity_modules/salmon/0.8.2/salmon.def
similarity index 100%
rename from src/singularity_modules/salmon/0.8.2/salmon.def
rename to src/.singularity_modules/salmon/0.8.2/salmon.def
diff --git a/src/singularity_modules/sambamba/0.6.7/build.sh b/src/.singularity_modules/sambamba/0.6.7/build.sh
similarity index 100%
rename from src/singularity_modules/sambamba/0.6.7/build.sh
rename to src/.singularity_modules/sambamba/0.6.7/build.sh
diff --git a/src/singularity_modules/sambamba/0.6.7/sambamba b/src/.singularity_modules/sambamba/0.6.7/sambamba
similarity index 100%
rename from src/singularity_modules/sambamba/0.6.7/sambamba
rename to src/.singularity_modules/sambamba/0.6.7/sambamba
diff --git a/src/singularity_modules/sambamba/0.6.7/sambamba.def b/src/.singularity_modules/sambamba/0.6.7/sambamba.def
similarity index 100%
rename from src/singularity_modules/sambamba/0.6.7/sambamba.def
rename to src/.singularity_modules/sambamba/0.6.7/sambamba.def
diff --git a/src/singularity_modules/sambamba/0.6.9/build.sh b/src/.singularity_modules/sambamba/0.6.9/build.sh
similarity index 100%
rename from src/singularity_modules/sambamba/0.6.9/build.sh
rename to src/.singularity_modules/sambamba/0.6.9/build.sh
diff --git a/src/singularity_modules/sambamba/0.6.9/sambamba b/src/.singularity_modules/sambamba/0.6.9/sambamba
similarity index 100%
rename from src/singularity_modules/sambamba/0.6.9/sambamba
rename to src/.singularity_modules/sambamba/0.6.9/sambamba
diff --git a/src/singularity_modules/sambamba/0.6.9/sambamba.def b/src/.singularity_modules/sambamba/0.6.9/sambamba.def
similarity index 100%
rename from src/singularity_modules/sambamba/0.6.9/sambamba.def
rename to src/.singularity_modules/sambamba/0.6.9/sambamba.def
diff --git a/src/singularity_modules/samblaster/0.1.24/build.sh b/src/.singularity_modules/samblaster/0.1.24/build.sh
similarity index 100%
rename from src/singularity_modules/samblaster/0.1.24/build.sh
rename to src/.singularity_modules/samblaster/0.1.24/build.sh
diff --git a/src/singularity_modules/samblaster/0.1.24/samblaster b/src/.singularity_modules/samblaster/0.1.24/samblaster
similarity index 100%
rename from src/singularity_modules/samblaster/0.1.24/samblaster
rename to src/.singularity_modules/samblaster/0.1.24/samblaster
diff --git a/src/singularity_modules/samblaster/0.1.24/samblaster.def b/src/.singularity_modules/samblaster/0.1.24/samblaster.def
similarity index 100%
rename from src/singularity_modules/samblaster/0.1.24/samblaster.def
rename to src/.singularity_modules/samblaster/0.1.24/samblaster.def
diff --git a/src/singularity_modules/samtools/1.7/build.sh b/src/.singularity_modules/samtools/1.7/build.sh
similarity index 100%
rename from src/singularity_modules/samtools/1.7/build.sh
rename to src/.singularity_modules/samtools/1.7/build.sh
diff --git a/src/singularity_modules/samtools/1.7/samtools b/src/.singularity_modules/samtools/1.7/samtools
similarity index 100%
rename from src/singularity_modules/samtools/1.7/samtools
rename to src/.singularity_modules/samtools/1.7/samtools
diff --git a/src/singularity_modules/samtools/1.7/samtools.def b/src/.singularity_modules/samtools/1.7/samtools.def
similarity index 100%
rename from src/singularity_modules/samtools/1.7/samtools.def
rename to src/.singularity_modules/samtools/1.7/samtools.def
diff --git a/src/singularity_modules/sratoolkit/2.8.2/build.sh b/src/.singularity_modules/sratoolkit/2.8.2/build.sh
similarity index 100%
rename from src/singularity_modules/sratoolkit/2.8.2/build.sh
rename to src/.singularity_modules/sratoolkit/2.8.2/build.sh
diff --git a/src/singularity_modules/sratoolkit/2.8.2/sratoolkit b/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit
similarity index 100%
rename from src/singularity_modules/sratoolkit/2.8.2/sratoolkit
rename to src/.singularity_modules/sratoolkit/2.8.2/sratoolkit
diff --git a/src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def b/src/.singularity_modules/sratoolkit/2.8.2/sratoolkit.def
similarity index 100%
rename from src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def
rename to src/.singularity_modules/sratoolkit/2.8.2/sratoolkit.def
diff --git a/src/singularity_modules/subread/1.6.4/build.sh b/src/.singularity_modules/subread/1.6.4/build.sh
similarity index 100%
rename from src/singularity_modules/subread/1.6.4/build.sh
rename to src/.singularity_modules/subread/1.6.4/build.sh
diff --git a/src/singularity_modules/subread/1.6.4/subread b/src/.singularity_modules/subread/1.6.4/subread
similarity index 100%
rename from src/singularity_modules/subread/1.6.4/subread
rename to src/.singularity_modules/subread/1.6.4/subread
diff --git a/src/singularity_modules/subread/1.6.4/subread.def b/src/.singularity_modules/subread/1.6.4/subread.def
similarity index 100%
rename from src/singularity_modules/subread/1.6.4/subread.def
rename to src/.singularity_modules/subread/1.6.4/subread.def
diff --git a/src/singularity_modules/tophat/2.1.1/build.sh b/src/.singularity_modules/tophat/2.1.1/build.sh
similarity index 100%
rename from src/singularity_modules/tophat/2.1.1/build.sh
rename to src/.singularity_modules/tophat/2.1.1/build.sh
diff --git a/src/singularity_modules/tophat/2.1.1/tophat b/src/.singularity_modules/tophat/2.1.1/tophat
similarity index 100%
rename from src/singularity_modules/tophat/2.1.1/tophat
rename to src/.singularity_modules/tophat/2.1.1/tophat
diff --git a/src/singularity_modules/tophat/2.1.1/tophat.def b/src/.singularity_modules/tophat/2.1.1/tophat.def
similarity index 100%
rename from src/singularity_modules/tophat/2.1.1/tophat.def
rename to src/.singularity_modules/tophat/2.1.1/tophat.def
diff --git a/src/singularity_modules/trimmomatic/0.36/build.sh b/src/.singularity_modules/trimmomatic/0.36/build.sh
similarity index 100%
rename from src/singularity_modules/trimmomatic/0.36/build.sh
rename to src/.singularity_modules/trimmomatic/0.36/build.sh
diff --git a/src/singularity_modules/trimmomatic/0.36/trimmomatic b/src/.singularity_modules/trimmomatic/0.36/trimmomatic
similarity index 100%
rename from src/singularity_modules/trimmomatic/0.36/trimmomatic
rename to src/.singularity_modules/trimmomatic/0.36/trimmomatic
diff --git a/src/singularity_modules/trimmomatic/0.36/trimmomatic.def b/src/.singularity_modules/trimmomatic/0.36/trimmomatic.def
similarity index 100%
rename from src/singularity_modules/trimmomatic/0.36/trimmomatic.def
rename to src/.singularity_modules/trimmomatic/0.36/trimmomatic.def
diff --git a/src/singularity_modules/ucsc/375/build.sh b/src/.singularity_modules/ucsc/375/build.sh
similarity index 100%
rename from src/singularity_modules/ucsc/375/build.sh
rename to src/.singularity_modules/ucsc/375/build.sh
diff --git a/src/singularity_modules/ucsc/375/ucsc b/src/.singularity_modules/ucsc/375/ucsc
similarity index 100%
rename from src/singularity_modules/ucsc/375/ucsc
rename to src/.singularity_modules/ucsc/375/ucsc
diff --git a/src/singularity_modules/ucsc/375/ucsc.def b/src/.singularity_modules/ucsc/375/ucsc.def
similarity index 100%
rename from src/singularity_modules/ucsc/375/ucsc.def
rename to src/.singularity_modules/ucsc/375/ucsc.def
diff --git a/src/singularity_modules/umi_tools/1.0.0/build.sh b/src/.singularity_modules/umi_tools/1.0.0/build.sh
similarity index 100%
rename from src/singularity_modules/umi_tools/1.0.0/build.sh
rename to src/.singularity_modules/umi_tools/1.0.0/build.sh
diff --git a/src/singularity_modules/umi_tools/1.0.0/umi_tools b/src/.singularity_modules/umi_tools/1.0.0/umi_tools
similarity index 100%
rename from src/singularity_modules/umi_tools/1.0.0/umi_tools
rename to src/.singularity_modules/umi_tools/1.0.0/umi_tools
diff --git a/src/singularity_modules/umi_tools/1.0.0/umi_tools.def b/src/.singularity_modules/umi_tools/1.0.0/umi_tools.def
similarity index 100%
rename from src/singularity_modules/umi_tools/1.0.0/umi_tools.def
rename to src/.singularity_modules/umi_tools/1.0.0/umi_tools.def
diff --git a/src/singularity_modules/urqt/d62c1f8/build.sh b/src/.singularity_modules/urqt/d62c1f8/build.sh
similarity index 100%
rename from src/singularity_modules/urqt/d62c1f8/build.sh
rename to src/.singularity_modules/urqt/d62c1f8/build.sh
diff --git a/src/singularity_modules/urqt/d62c1f8/urqt b/src/.singularity_modules/urqt/d62c1f8/urqt
similarity index 100%
rename from src/singularity_modules/urqt/d62c1f8/urqt
rename to src/.singularity_modules/urqt/d62c1f8/urqt
diff --git a/src/singularity_modules/urqt/d62c1f8/urqt.def b/src/.singularity_modules/urqt/d62c1f8/urqt.def
similarity index 100%
rename from src/singularity_modules/urqt/d62c1f8/urqt.def
rename to src/.singularity_modules/urqt/d62c1f8/urqt.def
diff --git a/src/.update_config.sh b/src/.update_config.sh
new file mode 100644
index 00000000..8d66be12
--- /dev/null
+++ b/src/.update_config.sh
@@ -0,0 +1,18 @@
+# update docker url
+fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|container = "|container = "lbmc/|g' -i {}
+
+# update singularity url
+fd ".*config" -E "nf_modules" src/ -x perl -pe 's|container = "lbmc/file://bin/(.*).img"|container = "lbmc/\1"|g' -i {}
+
+# update singularity config
+fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|\n\s*singularity {\n\s*singularity.enabled = true|\n  singularity {\n    singularity.enabled = true\n    singularity.cacheDir = "./bin/"|mg' -i {}
+
+# update in2p3 config
+fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|\n\s*ccin2p3 {\n\s*singularity.enabled = true|\n  ccin2p3 {\n    singularity.enabled = true\n    singularity.cacheDir = "/sps/lbmc/common/singularity/"|mg' -i {}
+fd ".*config" src/ -x perl -pe 's|container = "lbmc//sps/lbmc/common/singularity/(.*).img"|container = "lbmc/\1"|g' -i {}
+
+# we remove the ccin2p3_conda section
+fd ".*config" -E "nf_modules" src/ -x perl -0777pe "s|\s*ccin2p3_conda {.*ccin2p3 {\n|\n  ccin2p3 {\n|msg" -i {}
+
+# we update the psmn module to conda
+fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"\n\s*module = "(.*)/(.*)"|beforeScript = "source \$baseDir/.conda_psmn.sh"\n        conda = "\$baseDir/.conda_envs/\L\1_\2"|mg' -i {}
diff --git a/src/update_tools.sh b/src/.update_tools.sh
similarity index 100%
rename from src/update_tools.sh
rename to src/.update_tools.sh
diff --git a/src/conda_packages.sh b/src/conda_packages.sh
deleted file mode 100644
index f4be84f8..00000000
--- a/src/conda_packages.sh
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/bin/sh
-function install_env {
-  if [ ! -d "${CONDA_PREFIX}/envs/${1}_${2}" ]; then
-    conda create --yes --name ${1}_${2} ${3}=${2}
-  fi
-}
-
-install_env pigz 2.3.4 pigz
-install_env tophat 2.1.1 tophat
-install_env hisat2 2.0.0 hisat2
-install_env hisat2 2.1.0 hisat2
-install_env rsem 1.3.1 rsem
-install_env rsem 1.3.0 rsem
-install_env samblaster 0.1.24 samblaster
-install_env nextflow 0.25.1 nextflow
-install_env nextflow 19.01.0 nextflow
-install_env nextflow 0.32.0 nextflow
-install_env nextflow 0.28.2 nextflow
-install_env samtools 1.7 samtools
-install_env samtools 1.5 samtools
-install_env bowtie2 2.3.2 bowtie2
-install_env bowtie2 2.3.4.1 bowtie2
-install_env sratools 2.8.2 sra-tools
-install_env trimmomatic 0.36 trimmomatic
-install_env trimmomatic 0.39 trimmomatic
-install_env Python 3.6.1 Python
-install_env Python 2.7.13 Python
-install_env kallisto 0.44.0 kallisto
-install_env kallisto 0.43.1 kallisto
-install_env music 1.0.0 music
-install_env umitools 0.3.4 umitools
-install_env umi_tools 1.0.0 umi_tools
-install_env fastp 0.19.7 fastp
-install_env gatk 3.8 gatk
-install_env cutadapt 1.14 cutadapt
-install_env cutadapt 2.1 cutadapt
-install_env bioawk 1.0 bioawk
-install_env canu 1.7 canu
-install_env fastqc 0.11.5 fastqc
-install_env bedtools 2.25.0 bedtools
-install_env macs2 2.1.2 macs2
-install_env bcftools 1.7 bcftools
-install_env salmon 0.8.2 salmon
-install_env urqt d62c1f8 urqt
-install_env multiqc 0.9 multiqc
-install_env multiqc 1.7 multiqc
-install_env multiqc 1.0 multiqc
-install_env cdhit 4.6.8 cdhit
-install_env deeptools 3.0.2 deeptools
-install_env htseq 0.9.1 htseq
-install_env htseq 0.11.2 htseq
-install_env python 3.7 python
-install_env R 3.5.1 R
-install_env R 3.4.3 R
-install_env R 3.3.1 R
-install_env file handle 0.1.1 file handle
-install_env ncdu 1.13 ncdu
-install_env picard 2.18.11 picard
-install_env sambamba 0.6.7 sambamba
-install_env subread 1.6.4 subread
-
diff --git a/src/docker_modules/bcftools/1.7/docker_init.sh b/src/docker_modules/bcftools/1.7/docker_init.sh
deleted file mode 100755
index 6d19c689..00000000
--- a/src/docker_modules/bcftools/1.7/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/bcftools/1.7 -t 'bcftools:1.7'
diff --git a/src/docker_modules/bedtools/2.25.0/docker_init.sh b/src/docker_modules/bedtools/2.25.0/docker_init.sh
deleted file mode 100755
index 63da76f2..00000000
--- a/src/docker_modules/bedtools/2.25.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/bedtools/2.25.0 -t 'bedtools:2.25.0'
diff --git a/src/docker_modules/bioawk/1.0/docker_init.sh b/src/docker_modules/bioawk/1.0/docker_init.sh
deleted file mode 100755
index 23c16335..00000000
--- a/src/docker_modules/bioawk/1.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/bioawk/1.0 -t 'bioawk:1.0'
diff --git a/src/docker_modules/bowtie/1.2.2/docker_init.sh b/src/docker_modules/bowtie/1.2.2/docker_init.sh
deleted file mode 100755
index c8106dbf..00000000
--- a/src/docker_modules/bowtie/1.2.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/bowtie/1.2.2 -t 'bowtie:1.2.2'
diff --git a/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh b/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh
deleted file mode 100755
index 77141d11..00000000
--- a/src/docker_modules/bowtie2/2.3.4.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/bowtie2/2.3.4.1 -t 'bowtie2:2.3.4.1'
diff --git a/src/docker_modules/bwa/0.7.17/docker_init.sh b/src/docker_modules/bwa/0.7.17/docker_init.sh
deleted file mode 100755
index d2031220..00000000
--- a/src/docker_modules/bwa/0.7.17/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/bwa/0.7.17 -t 'bwa:0.7.17'
diff --git a/src/docker_modules/canu/1.6/docker_init.sh b/src/docker_modules/canu/1.6/docker_init.sh
deleted file mode 100755
index 5e0e3b44..00000000
--- a/src/docker_modules/canu/1.6/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/canu/1.6 -t 'canu:1.6'
diff --git a/src/docker_modules/cutadapt/1.14/docker_init.sh b/src/docker_modules/cutadapt/1.14/docker_init.sh
deleted file mode 100755
index 8edfebf5..00000000
--- a/src/docker_modules/cutadapt/1.14/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/cutadapt/1.14 -t 'cutadapt:1.14'
diff --git a/src/docker_modules/cutadapt/1.15/docker_init.sh b/src/docker_modules/cutadapt/1.15/docker_init.sh
deleted file mode 100755
index b3cf5413..00000000
--- a/src/docker_modules/cutadapt/1.15/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/cutadapt/1.15 -t 'cutadapt:1.15'
diff --git a/src/docker_modules/cutadapt/2.1/docker_init.sh b/src/docker_modules/cutadapt/2.1/docker_init.sh
deleted file mode 100755
index 33192004..00000000
--- a/src/docker_modules/cutadapt/2.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/cutadapt/2.1 -t 'cutadapt:2.1'
diff --git a/src/docker_modules/deeptools/3.0.2/docker_init.sh b/src/docker_modules/deeptools/3.0.2/docker_init.sh
deleted file mode 100755
index a2f152d2..00000000
--- a/src/docker_modules/deeptools/3.0.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/deeptools/3.0.2 -t 'deeptools:3.0.2'
diff --git a/src/docker_modules/deeptools/3.1.1/docker_init.sh b/src/docker_modules/deeptools/3.1.1/docker_init.sh
deleted file mode 100755
index 3c6782f0..00000000
--- a/src/docker_modules/deeptools/3.1.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/deeptools/3.1.1 -t 'deeptools:3.1.1'
diff --git a/src/docker_modules/fastp/0.19.7/docker_init.sh b/src/docker_modules/fastp/0.19.7/docker_init.sh
deleted file mode 100755
index 0480706a..00000000
--- a/src/docker_modules/fastp/0.19.7/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/fastp/0.19.7 -t 'fastp:0.19.7'
diff --git a/src/docker_modules/fastqc/0.11.5/docker_init.sh b/src/docker_modules/fastqc/0.11.5/docker_init.sh
deleted file mode 100755
index 0c02fb70..00000000
--- a/src/docker_modules/fastqc/0.11.5/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/fastqc/0.11.5 -t 'fastqc:0.11.5'
diff --git a/src/docker_modules/file_handle/0.1.1/docker_init.sh b/src/docker_modules/file_handle/0.1.1/docker_init.sh
deleted file mode 100755
index e7af3cb0..00000000
--- a/src/docker_modules/file_handle/0.1.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/file_handle/0.1.1 -t 'file_handle:0.1.1'
diff --git a/src/docker_modules/gatk/4.0.8.1/docker_init.sh b/src/docker_modules/gatk/4.0.8.1/docker_init.sh
deleted file mode 100755
index 31315f92..00000000
--- a/src/docker_modules/gatk/4.0.8.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/gatk/4.0.8.1 -t 'gatk:4.0.8.1'
diff --git a/src/docker_modules/hisat2/2.0.0/docker_init.sh b/src/docker_modules/hisat2/2.0.0/docker_init.sh
deleted file mode 100755
index 428e28c4..00000000
--- a/src/docker_modules/hisat2/2.0.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/hisat2/2.0.0 -t 'hisat2:2.0.0'
diff --git a/src/docker_modules/hisat2/2.1.0/docker_init.sh b/src/docker_modules/hisat2/2.1.0/docker_init.sh
deleted file mode 100755
index 3004f07a..00000000
--- a/src/docker_modules/hisat2/2.1.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/hisat2/2.1.0 -t 'hisat2:2.1.0'
diff --git a/src/docker_modules/htseq/0.11.2/docker_init.sh b/src/docker_modules/htseq/0.11.2/docker_init.sh
deleted file mode 100755
index 3d173e17..00000000
--- a/src/docker_modules/htseq/0.11.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/htseq/0.11.2 -t 'htseq:0.11.2'
diff --git a/src/docker_modules/htseq/0.8.0/docker_init.sh b/src/docker_modules/htseq/0.8.0/docker_init.sh
deleted file mode 100755
index be46648e..00000000
--- a/src/docker_modules/htseq/0.8.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/htseq/0.8.0 -t 'htseq:0.8.0'
diff --git a/src/docker_modules/kallisto/0.43.1/docker_init.sh b/src/docker_modules/kallisto/0.43.1/docker_init.sh
deleted file mode 100755
index 08241603..00000000
--- a/src/docker_modules/kallisto/0.43.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/kallisto/0.43.1 -t 'kallisto:0.43.1'
diff --git a/src/docker_modules/kallisto/0.44.0/docker_init.sh b/src/docker_modules/kallisto/0.44.0/docker_init.sh
deleted file mode 100755
index 9e9e8c91..00000000
--- a/src/docker_modules/kallisto/0.44.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/kallisto/0.44.0 -t 'kallisto:0.44.0'
diff --git a/src/docker_modules/macs2/2.1.2/docker_init.sh b/src/docker_modules/macs2/2.1.2/docker_init.sh
deleted file mode 100755
index 2cd63afd..00000000
--- a/src/docker_modules/macs2/2.1.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/macs2/2.1.2 -t 'macs2:2.1.2'
diff --git a/src/docker_modules/multiqc/1.0/docker_init.sh b/src/docker_modules/multiqc/1.0/docker_init.sh
deleted file mode 100755
index 4c6de82a..00000000
--- a/src/docker_modules/multiqc/1.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/multiqc/1.0 -t 'multiqc:1.0'
diff --git a/src/docker_modules/multiqc/1.7/docker_init.sh b/src/docker_modules/multiqc/1.7/docker_init.sh
deleted file mode 100755
index 67ff4536..00000000
--- a/src/docker_modules/multiqc/1.7/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/multiqc/1.7 -t 'multiqc:1.7'
diff --git a/src/docker_modules/music/6613c53/docker_init.sh b/src/docker_modules/music/6613c53/docker_init.sh
deleted file mode 100755
index 5daa39f1..00000000
--- a/src/docker_modules/music/6613c53/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/music/6613c53 -t 'music:6613c53'
diff --git a/src/docker_modules/picard/2.18.11/docker_init.sh b/src/docker_modules/picard/2.18.11/docker_init.sh
deleted file mode 100755
index 7546e343..00000000
--- a/src/docker_modules/picard/2.18.11/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/picard/2.18.11 -t 'picard:2.18.11'
diff --git a/src/docker_modules/pigz/2.4/docker_init.sh b/src/docker_modules/pigz/2.4/docker_init.sh
deleted file mode 100755
index 776a4c54..00000000
--- a/src/docker_modules/pigz/2.4/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/pigz/2.4 -t 'pigz:2.4'
diff --git a/src/docker_modules/python/3.8/docker_init.sh b/src/docker_modules/python/3.8/docker_init.sh
deleted file mode 100755
index c20b6603..00000000
--- a/src/docker_modules/python/3.8/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/python/3.8 -t 'python:3.8'
diff --git a/src/docker_modules/r/3.5.3/docker_init.sh b/src/docker_modules/r/3.5.3/docker_init.sh
deleted file mode 100755
index c054d37c..00000000
--- a/src/docker_modules/r/3.5.3/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/r/3.5.3 -t 'r:3.5.3'
diff --git a/src/docker_modules/rsem/1.3.0/docker_init.sh b/src/docker_modules/rsem/1.3.0/docker_init.sh
deleted file mode 100755
index 02d4bf9c..00000000
--- a/src/docker_modules/rsem/1.3.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/rsem/1.3.0 -t 'rsem:1.3.0'
diff --git a/src/docker_modules/salmon/0.8.2/docker_init.sh b/src/docker_modules/salmon/0.8.2/docker_init.sh
deleted file mode 100755
index 5abdc6b0..00000000
--- a/src/docker_modules/salmon/0.8.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/salmon/0.8.2 -t 'salmon:0.8.2'
diff --git a/src/docker_modules/sambamba/0.6.7/docker_init.sh b/src/docker_modules/sambamba/0.6.7/docker_init.sh
deleted file mode 100755
index 2db68c5b..00000000
--- a/src/docker_modules/sambamba/0.6.7/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/sambamba/0.6.7 -t 'sambamba:0.6.7'
diff --git a/src/docker_modules/sambamba/0.6.9/docker_init.sh b/src/docker_modules/sambamba/0.6.9/docker_init.sh
deleted file mode 100755
index f9a2f992..00000000
--- a/src/docker_modules/sambamba/0.6.9/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/sambamba/0.6.9 -t 'sambamba:0.6.9'
diff --git a/src/docker_modules/samblaster/0.1.24/docker_init.sh b/src/docker_modules/samblaster/0.1.24/docker_init.sh
deleted file mode 100755
index 24927903..00000000
--- a/src/docker_modules/samblaster/0.1.24/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/samblaster/0.1.24 -t 'samblaster:0.1.24'
diff --git a/src/docker_modules/samtools/1.7/docker_init.sh b/src/docker_modules/samtools/1.7/docker_init.sh
deleted file mode 100755
index 03dc62e9..00000000
--- a/src/docker_modules/samtools/1.7/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/samtools/1.7 -t 'samtools:1.7'
diff --git a/src/docker_modules/sratoolkit/2.8.2/docker_init.sh b/src/docker_modules/sratoolkit/2.8.2/docker_init.sh
deleted file mode 100755
index 234100e8..00000000
--- a/src/docker_modules/sratoolkit/2.8.2/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/sratoolkit/2.8.2 -t 'sratoolkit:2.8.2'
diff --git a/src/docker_modules/subread/1.6.4/docker_init.sh b/src/docker_modules/subread/1.6.4/docker_init.sh
deleted file mode 100755
index 9c2c6856..00000000
--- a/src/docker_modules/subread/1.6.4/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/subread/1.6.4 -t 'subread:1.6.4'
diff --git a/src/docker_modules/tophat/2.1.1/docker_init.sh b/src/docker_modules/tophat/2.1.1/docker_init.sh
deleted file mode 100755
index 4dd0937a..00000000
--- a/src/docker_modules/tophat/2.1.1/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/tophat/2.1.1 -t 'tophat:2.1.1'
diff --git a/src/docker_modules/trimmomatic/0.36/docker_init.sh b/src/docker_modules/trimmomatic/0.36/docker_init.sh
deleted file mode 100755
index 63bcdabf..00000000
--- a/src/docker_modules/trimmomatic/0.36/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/trimmomatic/0.36 -t 'trimmomatic:0.36'
diff --git a/src/docker_modules/ucsc/375/docker_init.sh b/src/docker_modules/ucsc/375/docker_init.sh
deleted file mode 100755
index ef314b42..00000000
--- a/src/docker_modules/ucsc/375/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/ucsc/375/ -t 'ucsc:375'
diff --git a/src/docker_modules/umi_tools/0.5.4/docker_init.sh b/src/docker_modules/umi_tools/0.5.4/docker_init.sh
deleted file mode 100755
index 8f0c4ea9..00000000
--- a/src/docker_modules/umi_tools/0.5.4/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/umi_tools/1.0.0/ -t 'umi_tools:1.0.0'
diff --git a/src/docker_modules/umi_tools/1.0.0/docker_init.sh b/src/docker_modules/umi_tools/1.0.0/docker_init.sh
deleted file mode 100755
index 8f0c4ea9..00000000
--- a/src/docker_modules/umi_tools/1.0.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/umi_tools/1.0.0/ -t 'umi_tools:1.0.0'
diff --git a/src/docker_modules/urqt/d62c1f8/docker_init.sh b/src/docker_modules/urqt/d62c1f8/docker_init.sh
deleted file mode 100755
index 4c6c5269..00000000
--- a/src/docker_modules/urqt/d62c1f8/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/urqt/d62c1f8 -t 'urqt:d62c1f8'
diff --git a/src/kallisto_index.pbs b/src/in2p3.pbs
similarity index 100%
rename from src/kallisto_index.pbs
rename to src/in2p3.pbs
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 1a225212..3372d452 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: fasta_from_bed {
-        container = "bedtools:2.25.0"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fasta_from_bed {
-        container = "file://bin/bedtools:2.25.0.img"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: fasta_from_bed {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bedtools/2.25.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/${CONDA_ENVS}bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fasta_from_bed {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bedtools_2.25.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fasta_from_bed {
-        container = "/sps/lbmc/common/singularity/bedtools:2.25.0.img"
+        container = "lbmc/bedtools:2.25.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 06b57209..32db140e 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -5,24 +5,25 @@ profiles {
     process {
       withName: index_fasta {
         cpus = 4
-        container = "bowtie:1.2.2"
+        container = "lbmc/bowtie:1.2.2"
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_fasta {
         cpus = 4
-        container = "file://bin/bowtie:1.2.2.img"
+        container = "lbmc/bowtie:1.2.2"
       }
     }
   }
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie/1.2.2"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie_1.2.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "20GB"
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
+        container = "lbmc/bowtie:1.2.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 61f40f9e..4aa916d0 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "bowtie:1.2.2"
+        container = "lbmc/bowtie:1.2.2"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "file://bin/bowtie:1.2.2.img"
+        container = "lbmc/bowtie:1.2.2"
       }
     }
   }
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie/1.2.2:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie/1.2.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
+        container = "lbmc/bowtie:1.2.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 61f40f9e..4aa916d0 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "bowtie:1.2.2"
+        container = "lbmc/bowtie:1.2.2"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "file://bin/bowtie:1.2.2.img"
+        container = "lbmc/bowtie:1.2.2"
       }
     }
   }
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie/1.2.2:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie/1.2.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
+        container = "lbmc/bowtie:1.2.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 2d52dc48..0fcb8507 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: index_fasta {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_fasta {
-        container = "file://bin/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 85655e48..7111d239 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 85655e48..7111d239 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index c970b5bb..b852e153 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: index_fasta {
-        container = "bwa:0.7.17"
+        container = "lbmc/bwa:0.7.17"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_fasta {
-        container = "file://bin/bwa:0.7.17.img"
+        container = "lbmc/bwa:0.7.17"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bwa/0.7.17"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bwa_0.7.17"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        container = "/sps/lbmc/common/singularity//bwa:0.7.17.img"
+        container = "lbmc/bwa:0.7.17"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index af4f9683..b493b5f4 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "bwa:0.7.17"
+        container = "lbmc/bwa:0.7.17"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/bwa:0.7.17.img"
+        container = "lbmc/bwa:0.7.17"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bwa/0.7.17"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bwa_0.7.17"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/bwa:0.7.17.img"
+        container = "lbmc/bwa:0.7.17"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 8add46ca..c6ad6528 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: adaptor_removal {
-        container = "cutadapt:2.1"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: adaptor_removal {
-        container = "file://bin/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: adaptor_removal {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "cutadapt/2.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/cutadapt_2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: adaptor_removal {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: adaptor_removal {
-        container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 8add46ca..c6ad6528 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: adaptor_removal {
-        container = "cutadapt:2.1"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: adaptor_removal {
-        container = "file://bin/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: adaptor_removal {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "cutadapt/2.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/cutadapt_2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: adaptor_removal {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: adaptor_removal {
-        container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 721d8805..edbee713 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: trimming {
-        container = "cutadapt:2.1"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: trimming {
-        container = "file://bin/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: trimming {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "cutadapt/2.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/cutadapt_2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,27 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: trimming {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: trimming {
-        container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 721d8805..edbee713 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: trimming {
-        container = "cutadapt:2.1"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: trimming {
-        container = "file://bin/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: trimming {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "cutadapt/2.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/cutadapt_2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,27 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: trimming {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: trimming {
-        container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
+        container = "lbmc/cutadapt:2.1"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 5be6a4cb..a30225b8 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -4,24 +4,25 @@ profiles {
     docker.enabled = true
     process {
       withName: index_bam {
-        container = "sambamba:0.6.7"
+        container = "lbmc/sambamba:0.6.7"
         cpus = 4
       }
       withName: bam_to_bigwig {
-        container = "deeptools:3.0.2"
+        container = "lbmc/deeptools:3.0.2"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_bam {
-        container = "file://bin/sambamba:0.6.7.img"
+        container = "lbmc/sambamba:0.6.7"
         cpus = 4
       }
       withName: bam_to_bigwig {
-        container = "file://bin/deeptools:3.0.2.img"
+        container = "lbmc/deeptools:3.0.2"
         cpus = 4
       }
     }
@@ -29,8 +30,8 @@ profiles {
   psmn{
     process{
       withName: index_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sambamba/0.6.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/sambamba_0.6.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -52,40 +53,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: bam_to_bigwig {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_bam {
-        container = "/sps/lbmc/common/singularity/sambamba:0.6.7.img"
+        container = "lbmc/sambamba:0.6.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -96,7 +70,7 @@ profiles {
         queue = 'huge'
       }
       withName: bam_to_bigwig {
-        container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
+        container = "lbmc/deeptools:3.0.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index b0986769..2e178044 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: compute_matrix {
-        container = "deeptools:3.0.2"
+        container = "lbmc/deeptools:3.0.2"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: compute_matrix {
-        container = "file://bin/deeptools:3.0.2.img"
+        container = "lbmc/deeptools:3.0.2"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: compute_matrix {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "deeptools/3.0.2"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/deeptools_3.0.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: compute_matrix {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: compute_matrix {
-        container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
+        container = "lbmc/deeptools:3.0.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index e9fe1504..cceb4746 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: plot_profile {
-        container = "deeptools:3.0.2"
+        container = "lbmc/deeptools:3.0.2"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: compute_matrix {
-        container = "file://bin/deeptools:3.0.2.img"
+        container = "lbmc/deeptools:3.0.2"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: plot_profile {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "deeptools/3.0.2"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/deeptools_3.0.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: plot_profile {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: plot_profile {
-        container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
+        container = "lbmc/deeptools:3.0.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index df041cb9..a9129ddb 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: fastp_fastq {
-        container = "fastp:0.19.7"
+        container = "lbmc/fastp:0.19.7"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fastp_fastq {
         cpus = 1
-        container = "file://bin/fastp:0.19.7.img"
+        container = "lbmc/fastp:0.19.7"
       }
     }
   }
   psmn{
     process{
       withName: fastp_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastp/0.19.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/fastp_0.19.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastp_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastp_fastq {
-        container = "/sps/lbmc/common/singularity/fastp:0.19.7.img"
+        container = "lbmc/fastp:0.19.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index df041cb9..a9129ddb 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: fastp_fastq {
-        container = "fastp:0.19.7"
+        container = "lbmc/fastp:0.19.7"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fastp_fastq {
         cpus = 1
-        container = "file://bin/fastp:0.19.7.img"
+        container = "lbmc/fastp:0.19.7"
       }
     }
   }
   psmn{
     process{
       withName: fastp_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastp/0.19.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/fastp_0.19.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastp_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastp_fastq {
-        container = "/sps/lbmc/common/singularity/fastp:0.19.7.img"
+        container = "lbmc/fastp:0.19.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 2ed15c54..e01fa5f5 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: fastqc_fastq {
-        container = "fastqc:0.11.5"
+        container = "lbmc/fastqc:0.11.5"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fastqc_fastq {
         cpus = 1
-        container = "file://bin/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
       }
     }
   }
   psmn{
     process{
       withName: fastqc_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastqc/0.11.5"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastqc_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastqc_fastq {
-        container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 2ed15c54..e01fa5f5 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: fastqc_fastq {
-        container = "fastqc:0.11.5"
+        container = "lbmc/fastqc:0.11.5"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fastqc_fastq {
         cpus = 1
-        container = "file://bin/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
       }
     }
   }
   psmn{
     process{
       withName: fastqc_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastqc/0.11.5"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastqc_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastqc_fastq {
-        container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index d97e7c74..6322661b 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -4,25 +4,26 @@ profiles {
     docker.enabled = true
     process {
       withName: index_fasta {
-        container = "hisat2:2.1.0"
+        container = "lbmc/hisat2:2.1.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_fasta {
         cpus = 4
-        container = "file://bin/hisat2:2.1.0.img"
+        container = "lbmc/hisat2:2.1.0"
       }
     }
   }
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "hisat2/2.1.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/hisat2_2.1.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "20GB"
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
+        container = "lbmc/hisat2:2.1.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index c0b9c808..860fc2f7 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -5,16 +5,17 @@ profiles {
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "hisat2:2.1.0"
+        container = "lbmc/hisat2:2.1.0"
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "file://bin/hisat2:2.1.0.img"
+        container = "lbmc/hisat2:2.1.0"
       }
     }
   }
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
+        container = "lbmc/hisat2:2.1.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index c0b9c808..860fc2f7 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -5,16 +5,17 @@ profiles {
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "hisat2:2.1.0"
+        container = "lbmc/hisat2:2.1.0"
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "file://bin/hisat2:2.1.0.img"
+        container = "lbmc/hisat2:2.1.0"
       }
     }
   }
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
+        container = "lbmc/hisat2:2.1.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index a04f0851..52c8ae86 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -4,24 +4,25 @@ profiles {
     docker.enabled = true
     process {
       withName: sort_bam {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 1
       }
       withName: counting {
-        container = "htseq:0.11.2"
+        container = "lbmc/htseq:0.11.2"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: sort_bam {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 1
       }
       withName: counting {
-        container = "file://bin/htseq:0.11.2.img"
+        container = "lbmc/htseq:0.11.2"
         cpus = 1
       }
     }
@@ -29,8 +30,8 @@ profiles {
   psmn{
     process{
       withName: sort_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -50,40 +51,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: sort_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: counting {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/htseq_0.11.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: sort_bam {
-        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -94,7 +68,7 @@ profiles {
         queue = 'huge'
       }
       withName: counting {
-        container = "/sps/lbmc/common/singularity/htseq:0.11.2.img"
+        container = "lbmc/htseq:0.11.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index b677b616..9bbba3d6 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withNamek index_fasta {
-        container = "kallisto:0.44.0"
+        container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_fasta {
-        container = "file://bin/kallisto:0.44.0.img"
+        container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "kallisto/0.44.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        container = "lbmc/kallisto:0.44.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 620e506d..5e1784b9 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "kallisto:0.44.0"
+        container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/kallisto:0.44.0.img"
+        container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "kallisto/0.44.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        container = "lbmc/kallisto:0.44.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 620e506d..5e1784b9 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "kallisto:0.44.0"
+        container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/kallisto:0.44.0.img"
+        container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "kallisto/0.44.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        container = "lbmc/kallisto:0.44.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 8e3965f8..747f26bb 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: peak_calling {
-        container = "macs2:2.1.2"
+        container = "lbmc/macs2:2.1.2"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: peak_calling {
-        container = "file://bin/macs2:2.1.2.img"
+        container = "lbmc/macs2:2.1.2"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: peak_calling {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "macs2/2.1.2"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/macs2_2.1.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/macs2_2.1.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: peak_calling {
-        container = "/sps/lbmc/common/singularity/macs2:2.1.2.img"
+        container = "lbmc/macs2:2.1.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 1825a135..0b220310 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -5,24 +5,25 @@ profiles {
     docker.enabled = true
     process {
       withName: fastqc_fastq {
-        container = "fastqc:0.11.5"
+        container = "lbmc/fastqc:0.11.5"
         cpus = 1
       }
       withName: multiqc {
-        container = "multiqc:1.7"
+        container = "lbmc/multiqc:1.7"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fastqc_fastq {
-        container = "file://bin/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
         cpus = 1
       }
       withName: multiqc {
-        container = "file://bin/multiqc:1.7.img"
+        container = "lbmc/multiqc:1.7"
         cpus = 1
       }
     }
@@ -30,8 +31,8 @@ profiles {
   psmn{
     process{
       withName: fastqc_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastqc/0.11.5"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -55,40 +56,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastqc_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: multiqc {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastq_fastqc {
-        container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -99,7 +73,7 @@ profiles {
         queue = 'huge'
       }
       withName: multiqc {
-        container = "/sps/lbmc/common/singularity/multiqc:1.7.img"
+        container = "lbmc/multiqc:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 6a2edfb6..80ecd7fd 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -4,24 +4,25 @@ profiles {
     docker.enabled = true
     process {
       withName: fastqc_fastq {
-        container = "fastqc:0.11.5"
+        container = "lbmc/fastqc:0.11.5"
         cpus = 1
       }
       withName: multiqc {
-        container = "multiqc:1.7"
+        container = "lbmc/multiqc:1.7"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: fastqc_fastq {
-        container = "file://bin/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
         cpus = 1
       }
       withName: multiqc {
-        container = "file://bin/multiqc:1.7.img"
+        container = "lbmc/multiqc:1.7"
         cpus = 1
       }
     }
@@ -29,8 +30,8 @@ profiles {
   psmn{
     process{
       withName: fastqc_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastqc/0.11.5"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -54,40 +55,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastqc_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: multiqc {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastq_fastqc {
-        container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+        container = "lbmc/fastqc:0.11.5"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -98,7 +72,7 @@ profiles {
         queue = 'huge'
       }
       withName: multiqc {
-        container = "/sps/lbmc/common/singularity/multiqc:1.7.img"
+        container = "lbmc/multiqc:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index dc46d8c8..01261907 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -4,32 +4,33 @@ profiles {
     docker.enabled = true
     process {
       withName: compute_mappability {
-        container = "music:6613c53"
+        container = "lbmc/music:6613c53"
         cpus = 1
       }
       withName: music_preprocessing {
-        container = "music:6613c53"
+        container = "lbmc/music:6613c53"
         cpus = 1
       }
       withName: music_computation{
-        container = "music:6613c53"
+        container = "lbmc/music:6613c53"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: compute_mappability {
-        container = "file://bin/music:6613c53.img"
+        container = "lbmc/music:6613c53"
         cpus = 1
       }
       withName: music_preprocessing {
-        container = "file://bin/music:6613c53.img"
+        container = "lbmc/music:6613c53"
         cpus = 1
       }
       withName: music_computation{
-        container = "file://bin/music:6613c53.img"
+        container = "lbmc/music:6613c53"
         cpus = 1
       }
     }
@@ -37,8 +38,8 @@ profiles {
   psmn{
     process{
       withName: compute_mappability {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "music/6613c53"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/music_6613c53"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -68,52 +69,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: compute_mappability {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: music_preprocessing {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: music_computation{
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: compute_mappability {
-        container = "/sps/lbmc/common/singularity/music:6613c53.img"
+        container = "lbmc/music:6613c53"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -124,7 +86,7 @@ profiles {
         queue = 'huge'
       }
       withName: music_preprocessing {
-        container = "/sps/lbmc/common/singularity/music:6613c53.img"
+        container = "lbmc/music:6613c53"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -135,7 +97,7 @@ profiles {
         queue = 'huge'
       }
       withName: music_computation{
-        container = "/sps/lbmc/common/singularity/music:6613c53.img"
+        container = "lbmc/music:6613c53"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index d58a310d..be6169e2 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: index_fasta {
-        container = "rsem:1.3.0"
+        container = "lbmc/rsem:1.3.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_fasta {
-        container = "file://bin/rsem:1.3.0.img"
+        container = "lbmc/rsem:1.3.0"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "rsem/1.3.0:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/rsem_1.3.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_fasta {
-        container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
+        container = "lbmc/rsem:1.3.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 75aae6ed..97502ecd 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "rsem:1.3.0"
+        container = "lbmc/rsem:1.3.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/rsem:1.3.0.img"
+        container = "lbmc/rsem:1.3.0"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "rsem/1.3.0:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/rsem_1.3.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
+        container = "lbmc/rsem:1.3.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 75aae6ed..97502ecd 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: mapping_fastq {
-        container = "rsem:1.3.0"
+        container = "lbmc/rsem:1.3.0"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: mapping_fastq {
-        container = "file://bin/rsem:1.3.0.img"
+        container = "lbmc/rsem:1.3.0"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "rsem/1.3.0:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/rsem_1.3.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: mapping_fastq {
-        container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
+        container = "lbmc/rsem:1.3.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 9199b7a4..95cb2371 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: index_bam {
-        container = "sambamba:0.6.9"
+        container = "lbmc/sambamba:0.6.9"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_bam {
-        container = "file://bin/sambamba:0.6.9.img"
+        container = "lbmc/sambamba:0.6.9"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sambamba/0.6.9"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/sambamba_0.6.9"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_bam {
-        container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
+        container = "lbmc/sambamba:0.6.9"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 0a71fc38..3dd3273b 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: sort_bam {
-        container = "sambamba:0.6.9"
+        container = "lbmc/sambamba:0.6.9"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: sort_bam {
-        container = "file://bin/sambamba:0.6.9.img"
+        container = "lbmc/sambamba:0.6.9"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: sort_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sambamba/0.6.9"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/sambamba_0.6.9"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 4
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: sort_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: sort_bam {
-        container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
+        container = "lbmc/sambamba:0.6.9"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 8a3e4ab5..c774bd7f 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: split_bam {
-        container = "sambamba:0.6.9"
+        container = "lbmc/sambamba:0.6.9"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: split_bam {
-        container = "file://bin/sambamba:0.6.9.img"
+        container = "lbmc/sambamba:0.6.9"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: split_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sambamba/0.6.9"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/sambamba_0.6.9"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: split_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: split_bam {
-        container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
+        container = "lbmc/sambamba:0.6.9"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 7fd05167..cd17da01 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: dedup_sam {
-        container = "samblaster:0.1.24"
+        container = "lbmc/samblaster:0.1.24"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: split_bam {
-        container = "file://bin/sambamba:0.6.7.img"
+        container = "lbmc/sambamba:0.6.7"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: dedup_sam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samblaster/0.1.24"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samblaster_0.1.24"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: dedup_sam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samblaster_0.1.24"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: dedup_sam {
-        container = "/sps/lbmc/common/singularity/sambamba:0.6.7.img"
+        container = "lbmc/sambamba:0.6.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index fc7a216c..a909fd16 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: filter_bam {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: filter_bam {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: filter_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: filter_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: filter_bam {
-        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 8b910b60..1ab10017 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: index_bam {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: index_bam {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: index_bam {
-        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index d5e06e31..d3bbfa8b 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: sort_bam {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: sort_bam {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: sort_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: sort_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: sort_bam {
-        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index c145bf33..56b1eafc 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: split_bam {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 2
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: split_bam {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 2
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: split_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: split_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: split_bam {
-        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index ee6ed1fa..e01b71bc 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: fastq_dump {
-        container = "sratoolkit:2.8.2"
+        container = "lbmc/sratoolkit:2.8.2"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: split_bam {
-        container = "file://bin/sratoolkit:2.8.2.img"
+        container = "lbmc/sratoolkit:2.8.2"
         cpus = 1
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: fastq_dump {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sratoolkit/2.8.2"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/sratoolkit_2.8.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -32,28 +33,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastq_dump {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/sratoolkit_2.8.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: fastq_dump {
-        container = "/sps/lbmc/common/singularity/sratoolkit:2.8.2.img"
+        container = "lbmc/sratoolkit:2.8.2"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index 19f20463..f0153ffa 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -4,24 +4,25 @@ profiles {
     docker.enabled = true
     process {
       withName: sort_bam {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 1
       }
       withName: counting {
-        container = "subread:1.6.4"
+        container = "lbmc/subread:1.6.4"
         cpus = 1
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: sort_bam {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 1
       }
       withName: counting {
-        container = "file://bin/subread:1.6.4.img"
+        container = "lbmc/subread:1.6.4"
         cpus = 1
       }
     }
@@ -29,8 +30,8 @@ profiles {
   psmn{
     process{
       withName: sort_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -50,40 +51,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: sort_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: counting {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/subread_1.6.4"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: sort_bam {
-        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
@@ -94,7 +68,7 @@ profiles {
         queue = 'huge'
       }
       withName: counting {
-        container = "/sps/lbmc/common/singularity/subread:1.6.4.img"
+        container = "lbmc/subread:1.6.4"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index dbe4e11c..4d8b855f 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -5,24 +5,25 @@ profiles {
     process {
       withName: trimming {
         cpus = 4
-        container = "urqt:d62c1f8"
+        container = "lbmc/urqt:d62c1f8"
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: trimming {
         cpus = 4
-        container = "file://bin/urqt:d62c1f8.img"
+        container = "lbmc/urqt:d62c1f8"
       }
     }
   }
   psmn{
     process{
       withName: trimming {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "urqt/d62c1f8"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "5GB"
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: trimming {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/urqt_d62c1f8"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: trimming {
-        container = "/sps/lbmc/common/singularity/urqt:d62c1f8.img"
+        container = "lbmc/urqt:d62c1f8"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 016d6503..b8b8fc16 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -4,16 +4,17 @@ profiles {
     docker.enabled = true
     process {
       withName: trimming {
-        container = "urqt:d62c1f8"
+        container = "lbmc/urqt:d62c1f8"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: trimming {
-        container = "file://bin/urqt:d62c1f8.img"
+        container = "lbmc/urqt:d62c1f8"
         cpus = 4
       }
     }
@@ -21,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: trimming {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "urqt/d62c1f8"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16
@@ -33,28 +34,13 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: trimming {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/urqt_d62c1f8"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
+    singularity.cacheDir = "/sps/lbmc/common/singularity/"
     singularity.runOptions = "--bind /pbs,/sps,/scratch"
     process{
       withName: trimming {
-        container = "/sps/lbmc/common/singularity/urqt:d62c1f8.img"
+        container = "lbmc/urqt:d62c1f8"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
diff --git a/src/psmn_modules b/src/psmn_modules
deleted file mode 160000
index 8a86db97..00000000
--- a/src/psmn_modules
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 8a86db97eb89833a88b1ee876880cb1c07ce8565
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 96add9d1..453e7b7e 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -4,112 +4,113 @@ profiles {
     docker.enabled = true
     process {
       withName: build_synthetic_bed {
-        container = "bedtools:2.25.0"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
       withName: fasta_from_bed {
-        container = "bedtools:2.25.0"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
       withName: index_fasta {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: mapping_fastq_paired {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: bam_2_fastq_paired {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: filter_bam_paired {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: sort_bam_paired {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: index_bam_paired {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: mapping_fastq_single {
-        container = "bowtie2:2.3.4.1"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: bam_2_fastq_single {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: filter_bam_single {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: sort_bam_single {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: index_bam_single {
-        container = "samtools:1.7"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
   }
   singularity {
     singularity.enabled = true
+    singularity.cacheDir = "./bin/"
     process {
       withName: build_synthetic_bed {
-        container = "file://bin/bedtools:2.25.0.img"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
       withName: fasta_from_bed {
-        container = "file://bin/bedtools:2.25.0.img"
+        container = "lbmc/bedtools:2.25.0"
         cpus = 1
       }
       withName: index_fasta {
-        container = "file://bin/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: mapping_fastq_single {
-        container = "file://bin/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: mapping_fastq_paired {
-        container = "file://bin/bowtie2:2.3.4.1.img"
+        container = "lbmc/bowtie2:2.3.4.1"
         cpus = 4
       }
       withName: bam_2_fastq_paired {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: filter_bam_paired {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: sort_bam_paired {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: index_bam_paired {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: bam_2_fastq_single {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: filter_bam_single {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: sort_bam_single {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
       withName: index_bam_single {
-        container = "file://bin/samtools:1.7.img"
+        container = "lbmc/samtools:1.7"
         cpus = 4
       }
     }
@@ -117,8 +118,8 @@ profiles {
   psmn {
     process{
       withName: build_synthetic_bed {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bedtools/2.25.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 1
@@ -127,8 +128,8 @@ profiles {
         queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
       }
       withName: fasta_from_bed {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bedtools/2.25.0"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 1
@@ -137,8 +138,8 @@ profiles {
         queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
       }
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -148,8 +149,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: mapping_fastq_paired {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -159,8 +160,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: bam_2_fastq_paired {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -170,8 +171,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: sort_bam_paired {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -181,8 +182,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: index_bam_paired {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -192,8 +193,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: mapping_fastq_single {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1:samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -203,8 +204,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: bam_2_fastq_single {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -214,8 +215,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: sort_bam_single {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -225,8 +226,8 @@ profiles {
         penv = 'openmp16'
       }
       withName: index_bam_single {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
-- 
GitLab