From b4af1b0e18b4e70c8eaf00c49f535e80cfe32b94 Mon Sep 17 00:00:00 2001
From: xgrand <157-xgrand@users.noreply.gitbio.ens-lyon.fr>
Date: Fri, 30 Jul 2021 16:03:45 +0200
Subject: [PATCH] fisrt
---
.gitignore | 5 +-
.../alntools/dd96682/docker_init.sh | 0
.../bamutils/1.0.14/docker_init.sh | 0
.../bcftools/1.7/docker_init.sh | 0
.../bedops/2.4.39/docker_init.sh | 0
.../bedtools/2.25.0/docker_init.sh | 0
.../bedtools/2.30.0/docker_init.sh | 0
src/.docker_modules/bioawk/1.0/docker_init.sh | 0
.../bowtie/1.2.2/docker_init.sh | 0
.../bowtie2/2.3.4.1/docker_init.sh | 0
src/.docker_modules/bwa/0.7.17/docker_init.sh | 0
src/.docker_modules/canu/1.6/docker_init.sh | 0
.../crossmap/0.4.1/docker_init.sh | 0
.../cutadapt/1.14/docker_init.sh | 0
.../cutadapt/1.15/docker_init.sh | 0
.../cutadapt/2.1/docker_init.sh | 0
.../deeptools/3.0.2/docker_init.sh | 0
.../deeptools/3.1.1/docker_init.sh | 0
.../deeptools/3.5.0/docker_init.sh | 0
.../deeptools/3.5.1/docker_init.sh | 0
src/.docker_modules/docker_push.sh | 0
.../emase-zero/0.3.1/docker_init.sh | 0
.../emase/0.10.16/docker_init.sh | 0
.../fastp/0.19.7/docker_init.sh | 0
.../fastp/0.20.1/docker_init.sh | 0
.../fastqc/0.11.5/docker_init.sh | 0
.../file_handle/0.1.1/docker_init.sh | 0
.../flexi_splitter/1.0.2/docker_init.sh | 0
.../freebayes/1.3.2/docker_init.sh | 0
.../g2gtools/0.2.7/docker_init.sh | 0
.../g2gtools/0.2.8/docker_init.sh | 0
src/.docker_modules/gatk/3.8.0/docker_init.sh | 0
.../gatk/4.0.8.1/docker_init.sh | 0
.../gffread/0.11.8/docker_init.sh | 0
.../gffread/0.12.2/docker_init.sh | 0
.../hisat2/2.0.0/docker_init.sh | 0
.../hisat2/2.1.0/docker_init.sh | 0
.../htseq/0.13.5/docker_init.sh | 0
.../htseq/0.8.0/docker_init.sh | 0
.../kallisto/0.43.1/docker_init.sh | 0
.../kallisto/0.44.0/docker_init.sh | 0
.../kallistobustools/0.24.4/docker_init.sh | 0
.../kallistobustools/0.39.3/docker_init.sh | 0
src/.docker_modules/kb/0.26.0/docker_init.sh | 0
src/.docker_modules/kb/0.26.0/t2g.py | 0
src/.docker_modules/kb/0.26.3/docker_init.sh | 0
src/.docker_modules/kb/0.26.3/t2g.py | 0
src/.docker_modules/last/1060/docker_init.sh | 0
.../liftover/357/docker_init.sh | 0
.../macs2/2.1.2/docker_init.sh | 0
.../macs3/3.0.0a6/docker_init.sh | 0
.../minimap2/2.17/docker_init.sh | 0
.../multiqc/1.0/docker_init.sh | 0
.../multiqc/1.7/docker_init.sh | 0
.../multiqc/1.9/docker_init.sh | 0
.../music/6613c53/docker_init.sh | 0
.../pandoc/2.11/docker_init.sh | 0
.../picard/2.18.11/docker_init.sh | 0
src/.docker_modules/pigz/2.4/docker_init.sh | 0
src/.docker_modules/python/3.8/docker_init.sh | 0
.../r-base/3.5.3/docker_init.sh | 0
.../r-base/3.6.2/docker_init.sh | 0
.../r-base/4.0.0/docker_init.sh | 0
.../r-base/4.0.2/docker_init.sh | 0
.../r-base/4.0.3/docker_init.sh | 0
src/.docker_modules/rsem/1.3.0/docker_init.sh | 0
.../sabre/039a55e/docker_init.sh | 0
.../salmon/0.8.2/docker_init.sh | 0
.../sambamba/0.6.7/docker_init.sh | 0
.../sambamba/0.6.9/docker_init.sh | 0
.../samblaster/0.1.24/docker_init.sh | 0
.../samtools/1.11/docker_init.sh | 0
.../samtools/1.7/docker_init.sh | 0
.../sratoolkit/2.8.2/docker_init.sh | 0
src/.docker_modules/star/2.5.3/docker_init.sh | 0
.../star/2.7.3a/docker_init.sh | 0
.../subread/1.6.4/docker_init.sh | 0
.../tophat/2.1.1/docker_init.sh | 0
.../trimmomatic/0.36/docker_init.sh | 0
src/.docker_modules/ucsc/375/docker_init.sh | 0
src/.docker_modules/ucsc/400/docker_init.sh | 0
src/.docker_modules/ucsc/407/docker_init.sh | 0
.../umi_tools/0.5.4/docker_init.sh | 0
.../umi_tools/1.0.0/docker_init.sh | 0
.../urqt/d62c1f8/docker_init.sh | 0
src/.singularity_in2p3 | 1 -
src/.singularity_psmn | 1 -
src/chipster.nf | 136 +++++
src/example_marseq.nf | 87 ----
src/example_variant_calling.nf | 36 --
src/fasta_sampler.nf | 18 -
src/install_nextflow.sh | 0
src/nextflow | 465 ++++++++++++++++++
src/nextflow.config | 2 -
src/nf_functions/control_ip_processing.nf | 24 +
src/nf_functions/reads_processing.nf | 5 +
src/nf_modules/multiqc/main.nf | 2 +-
src/solution_RNASeq.nf | 34 --
src/training_dataset.config | 370 --------------
src/training_dataset.nf | 308 ------------
100 files changed, 634 insertions(+), 860 deletions(-)
mode change 100755 => 100644 src/.docker_modules/alntools/dd96682/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/bamutils/1.0.14/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/bcftools/1.7/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/bedops/2.4.39/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/bedtools/2.25.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/bedtools/2.30.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/bioawk/1.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/bowtie/1.2.2/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/bwa/0.7.17/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/canu/1.6/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/crossmap/0.4.1/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/cutadapt/1.14/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/cutadapt/1.15/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/cutadapt/2.1/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/deeptools/3.0.2/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/deeptools/3.1.1/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/deeptools/3.5.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/deeptools/3.5.1/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/docker_push.sh
mode change 100755 => 100644 src/.docker_modules/emase-zero/0.3.1/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/emase/0.10.16/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/fastp/0.19.7/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/fastp/0.20.1/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/fastqc/0.11.5/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/file_handle/0.1.1/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/flexi_splitter/1.0.2/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/freebayes/1.3.2/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/g2gtools/0.2.7/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/g2gtools/0.2.8/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/gatk/3.8.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/gatk/4.0.8.1/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/gffread/0.11.8/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/gffread/0.12.2/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/hisat2/2.0.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/hisat2/2.1.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/htseq/0.13.5/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/htseq/0.8.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/kallisto/0.43.1/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/kallisto/0.44.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/kallistobustools/0.24.4/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/kallistobustools/0.39.3/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/kb/0.26.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/kb/0.26.0/t2g.py
mode change 100755 => 100644 src/.docker_modules/kb/0.26.3/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/kb/0.26.3/t2g.py
mode change 100755 => 100644 src/.docker_modules/last/1060/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/liftover/357/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/macs2/2.1.2/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/macs3/3.0.0a6/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/minimap2/2.17/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/multiqc/1.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/multiqc/1.7/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/multiqc/1.9/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/music/6613c53/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/pandoc/2.11/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/picard/2.18.11/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/pigz/2.4/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/python/3.8/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/r-base/3.5.3/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/r-base/3.6.2/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/r-base/4.0.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/r-base/4.0.2/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/r-base/4.0.3/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/rsem/1.3.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/sabre/039a55e/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/salmon/0.8.2/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/sambamba/0.6.7/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/sambamba/0.6.9/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/samblaster/0.1.24/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/samtools/1.11/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/samtools/1.7/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/star/2.5.3/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/star/2.7.3a/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/subread/1.6.4/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/tophat/2.1.1/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/trimmomatic/0.36/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/ucsc/375/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/ucsc/400/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/ucsc/407/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/umi_tools/0.5.4/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/umi_tools/1.0.0/docker_init.sh
mode change 100755 => 100644 src/.docker_modules/urqt/d62c1f8/docker_init.sh
delete mode 120000 src/.singularity_in2p3
delete mode 120000 src/.singularity_psmn
create mode 100644 src/chipster.nf
delete mode 100644 src/example_marseq.nf
delete mode 100644 src/example_variant_calling.nf
delete mode 100644 src/fasta_sampler.nf
mode change 100755 => 100644 src/install_nextflow.sh
create mode 100644 src/nextflow
create mode 100644 src/nf_functions/control_ip_processing.nf
create mode 100644 src/nf_functions/reads_processing.nf
delete mode 100644 src/solution_RNASeq.nf
delete mode 100644 src/training_dataset.config
delete mode 100644 src/training_dataset.nf
diff --git a/.gitignore b/.gitignore
index cb95d125..14809a5a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,7 @@
-nextflow
+nextflow/
.nextflow.log*
.nextflow/
work/
-results
+results/
workspace.code-workspace
+public/
diff --git a/src/.docker_modules/alntools/dd96682/docker_init.sh b/src/.docker_modules/alntools/dd96682/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/bamutils/1.0.14/docker_init.sh b/src/.docker_modules/bamutils/1.0.14/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/bcftools/1.7/docker_init.sh b/src/.docker_modules/bcftools/1.7/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/bedops/2.4.39/docker_init.sh b/src/.docker_modules/bedops/2.4.39/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/bedtools/2.25.0/docker_init.sh b/src/.docker_modules/bedtools/2.25.0/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/bedtools/2.30.0/docker_init.sh b/src/.docker_modules/bedtools/2.30.0/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/bioawk/1.0/docker_init.sh b/src/.docker_modules/bioawk/1.0/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/bowtie/1.2.2/docker_init.sh b/src/.docker_modules/bowtie/1.2.2/docker_init.sh
old mode 100755
new mode 100644
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
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/bwa/0.7.17/docker_init.sh b/src/.docker_modules/bwa/0.7.17/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/canu/1.6/docker_init.sh b/src/.docker_modules/canu/1.6/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/crossmap/0.4.1/docker_init.sh b/src/.docker_modules/crossmap/0.4.1/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/cutadapt/1.14/docker_init.sh b/src/.docker_modules/cutadapt/1.14/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/cutadapt/1.15/docker_init.sh b/src/.docker_modules/cutadapt/1.15/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/cutadapt/2.1/docker_init.sh b/src/.docker_modules/cutadapt/2.1/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/deeptools/3.0.2/docker_init.sh b/src/.docker_modules/deeptools/3.0.2/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/deeptools/3.1.1/docker_init.sh b/src/.docker_modules/deeptools/3.1.1/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/deeptools/3.5.0/docker_init.sh b/src/.docker_modules/deeptools/3.5.0/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/deeptools/3.5.1/docker_init.sh b/src/.docker_modules/deeptools/3.5.1/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/docker_push.sh b/src/.docker_modules/docker_push.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/emase-zero/0.3.1/docker_init.sh b/src/.docker_modules/emase-zero/0.3.1/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/emase/0.10.16/docker_init.sh b/src/.docker_modules/emase/0.10.16/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/fastp/0.19.7/docker_init.sh b/src/.docker_modules/fastp/0.19.7/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/fastp/0.20.1/docker_init.sh b/src/.docker_modules/fastp/0.20.1/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/fastqc/0.11.5/docker_init.sh b/src/.docker_modules/fastqc/0.11.5/docker_init.sh
old mode 100755
new mode 100644
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
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/flexi_splitter/1.0.2/docker_init.sh b/src/.docker_modules/flexi_splitter/1.0.2/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/freebayes/1.3.2/docker_init.sh b/src/.docker_modules/freebayes/1.3.2/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/g2gtools/0.2.7/docker_init.sh b/src/.docker_modules/g2gtools/0.2.7/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/g2gtools/0.2.8/docker_init.sh b/src/.docker_modules/g2gtools/0.2.8/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/gatk/3.8.0/docker_init.sh b/src/.docker_modules/gatk/3.8.0/docker_init.sh
old mode 100755
new mode 100644
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
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/gffread/0.11.8/docker_init.sh b/src/.docker_modules/gffread/0.11.8/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/gffread/0.12.2/docker_init.sh b/src/.docker_modules/gffread/0.12.2/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/hisat2/2.0.0/docker_init.sh b/src/.docker_modules/hisat2/2.0.0/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/hisat2/2.1.0/docker_init.sh b/src/.docker_modules/hisat2/2.1.0/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/htseq/0.13.5/docker_init.sh b/src/.docker_modules/htseq/0.13.5/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/htseq/0.8.0/docker_init.sh b/src/.docker_modules/htseq/0.8.0/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/kallisto/0.43.1/docker_init.sh b/src/.docker_modules/kallisto/0.43.1/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/kallisto/0.44.0/docker_init.sh b/src/.docker_modules/kallisto/0.44.0/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/kallistobustools/0.24.4/docker_init.sh b/src/.docker_modules/kallistobustools/0.24.4/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/kallistobustools/0.39.3/docker_init.sh b/src/.docker_modules/kallistobustools/0.39.3/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/kb/0.26.0/docker_init.sh b/src/.docker_modules/kb/0.26.0/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/kb/0.26.0/t2g.py b/src/.docker_modules/kb/0.26.0/t2g.py
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/kb/0.26.3/docker_init.sh b/src/.docker_modules/kb/0.26.3/docker_init.sh
old mode 100755
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diff --git a/src/.docker_modules/kb/0.26.3/t2g.py b/src/.docker_modules/kb/0.26.3/t2g.py
old mode 100755
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diff --git a/src/.docker_modules/last/1060/docker_init.sh b/src/.docker_modules/last/1060/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/liftover/357/docker_init.sh b/src/.docker_modules/liftover/357/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/macs2/2.1.2/docker_init.sh b/src/.docker_modules/macs2/2.1.2/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/macs3/3.0.0a6/docker_init.sh b/src/.docker_modules/macs3/3.0.0a6/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/minimap2/2.17/docker_init.sh b/src/.docker_modules/minimap2/2.17/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/multiqc/1.0/docker_init.sh b/src/.docker_modules/multiqc/1.0/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/multiqc/1.7/docker_init.sh b/src/.docker_modules/multiqc/1.7/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/multiqc/1.9/docker_init.sh b/src/.docker_modules/multiqc/1.9/docker_init.sh
old mode 100755
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diff --git a/src/.docker_modules/music/6613c53/docker_init.sh b/src/.docker_modules/music/6613c53/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/pandoc/2.11/docker_init.sh b/src/.docker_modules/pandoc/2.11/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/picard/2.18.11/docker_init.sh b/src/.docker_modules/picard/2.18.11/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/pigz/2.4/docker_init.sh b/src/.docker_modules/pigz/2.4/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/python/3.8/docker_init.sh b/src/.docker_modules/python/3.8/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/r-base/3.5.3/docker_init.sh b/src/.docker_modules/r-base/3.5.3/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/r-base/3.6.2/docker_init.sh b/src/.docker_modules/r-base/3.6.2/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/r-base/4.0.0/docker_init.sh b/src/.docker_modules/r-base/4.0.0/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/r-base/4.0.2/docker_init.sh b/src/.docker_modules/r-base/4.0.2/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/r-base/4.0.3/docker_init.sh b/src/.docker_modules/r-base/4.0.3/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/rsem/1.3.0/docker_init.sh b/src/.docker_modules/rsem/1.3.0/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/sabre/039a55e/docker_init.sh b/src/.docker_modules/sabre/039a55e/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/salmon/0.8.2/docker_init.sh b/src/.docker_modules/salmon/0.8.2/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/sambamba/0.6.7/docker_init.sh b/src/.docker_modules/sambamba/0.6.7/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/sambamba/0.6.9/docker_init.sh b/src/.docker_modules/sambamba/0.6.9/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/samblaster/0.1.24/docker_init.sh b/src/.docker_modules/samblaster/0.1.24/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/samtools/1.11/docker_init.sh b/src/.docker_modules/samtools/1.11/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/samtools/1.7/docker_init.sh b/src/.docker_modules/samtools/1.7/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh b/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/star/2.5.3/docker_init.sh b/src/.docker_modules/star/2.5.3/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/star/2.7.3a/docker_init.sh b/src/.docker_modules/star/2.7.3a/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/subread/1.6.4/docker_init.sh b/src/.docker_modules/subread/1.6.4/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/tophat/2.1.1/docker_init.sh b/src/.docker_modules/tophat/2.1.1/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/trimmomatic/0.36/docker_init.sh b/src/.docker_modules/trimmomatic/0.36/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/ucsc/375/docker_init.sh b/src/.docker_modules/ucsc/375/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/ucsc/400/docker_init.sh b/src/.docker_modules/ucsc/400/docker_init.sh
old mode 100755
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diff --git a/src/.docker_modules/ucsc/407/docker_init.sh b/src/.docker_modules/ucsc/407/docker_init.sh
old mode 100755
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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
old mode 100755
new mode 100644
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
old mode 100755
new mode 100644
diff --git a/src/.docker_modules/urqt/d62c1f8/docker_init.sh b/src/.docker_modules/urqt/d62c1f8/docker_init.sh
old mode 100755
new mode 100644
diff --git a/src/.singularity_in2p3 b/src/.singularity_in2p3
deleted file mode 120000
index 7f86c054..00000000
--- a/src/.singularity_in2p3
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/
\ No newline at end of file
diff --git a/src/.singularity_psmn b/src/.singularity_psmn
deleted file mode 120000
index 58b1c912..00000000
--- a/src/.singularity_psmn
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/abc/singularity/
\ No newline at end of file
diff --git a/src/chipster.nf b/src/chipster.nf
new file mode 100644
index 00000000..2546e99a
--- /dev/null
+++ b/src/chipster.nf
@@ -0,0 +1,136 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+/* ChIPseq pipeline :
+ * Pipeline that analyses ChIPseq data
+ * Preprocessing, filtration, alignment, peak calling...
+*/
+
+/*
+ ****************************************************************
+ parameters
+ ****************************************************************
+*/
+
+/*
+params.paired_end = true
+/* false for single end data, true for paired-end data
+
+@type: Boolean
+*/
+
+params.fastq = "data/tinyTestDataset/fastq/*_{1,2}.fastq"
+/* Fastq files containing ribosome footprint
+
+@type: Files
+*/
+
+params.genome = "data/tinyTestDataset/*.fasta"
+/* A genome file
+
+@type: File
+*/
+
+/*
+params.folder = "project"
+/* project output folder
+
+@Type: String
+*/
+
+/*
+ ****************************************************************
+ Logs
+ ****************************************************************
+*/
+
+log.info "fastq files : ${params.fastq}"
+log.info "genome files : ${params.genome}"
+
+/*
+log.info "paired-end data: ${params.paired_end}"
+log.info "output folder results/${params.folder}"
+*/
+
+/*
+ ****************************************************************
+ Channel definitions
+ ****************************************************************
+*/
+
+/* Raw reads fastq */
+Channel
+ .fromFilePairs( params.fastq )
+ .set { fastq_files }
+
+/* Reference Genome fasa file */
+/* Previous in .fromPath but raise an error : WARN: Input tuple does not
+ match input set cardinality declared by process `index_fasta`
+ -- offending value: /home/xavier/Scripts/Pipelines/ChIPster/data/tinyTestDataset/reference.fasta
+*/
+
+Channel
+ .fromFilePairs( params.genome, size: -1 )
+ .set { genome_file }
+
+/*
+ ****************************************************************
+ Imports
+ ****************************************************************
+*/
+
+fastqc_mod = "./nf_modules/fastqc/main.nf"
+include { fastp_default } from "./nf_modules/fastp/main.nf"
+include { fastqc_fastq as fastqc_raw } from fastqc_mod addParams(out: '01_fastqc')
+include { fastqc_fastq as fastqc_preprocessed } from fastqc_mod addParams(out: '02_fastqc_preprocessed')
+include { multiqc } from './nf_modules/multiqc/main.nf' addParams(multiqc_out: "QC/")
+include { index_fasta } from "./nf_modules/bowtie2/main.nf"
+include { mapping_fastq } from "./nf_modules/bowtie2/main.nf"
+include { filter_bam_quality } from "./nf_modules/samtools/main.nf"
+include { sort_bam } from "./nf_modules/samtools/main.nf"
+include { index_bam } from "./nf_modules/samtools/main.nf"
+include { bam_to_bigwig } from "./nf_modules/deeptools/main.nf"
+include { peak_calling } from "./nf_modules/macs3/main.nf"
+
+/*
+ ****************************************************************
+ Workflow
+ ****************************************************************
+*/
+
+workflow {
+ // fastp
+ fastp_default(fastq_files)
+ // fastqc_rawdata
+ fastqc_raw(fastq_files)
+ // fastqc_processed
+ fastqc_preprocessed(fastp_default.out.fastq)
+ // multiqc
+ multiqc(
+ fastqc_raw.out.report
+ .mix(
+ fastqc_preprocessed.out.report
+ ).collect()
+ )
+ // index reference genome
+ index_fasta(genome_file)
+
+ // mapping preprocessed reads
+ mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
+
+ // filter bam - remove reads with quality <30
+ filter_bam_quality(mapping_fastq.out.bam)
+
+ // samtools_sort
+ sort_bam(filter_bam_quality.out.bam)
+
+ // samtools_index
+ index_bam(sort_bam.out.bam.collect())
+
+ // Create a bigwig file
+ bam_to_bigwig(index_bam.out.bam_idx)
+
+ // peak calling using MACS3
+ // peak_calling(bam_to_bigwig.out.bw)
+}
diff --git a/src/example_marseq.nf b/src/example_marseq.nf
deleted file mode 100644
index 821ebd99..00000000
--- a/src/example_marseq.nf
+++ /dev/null
@@ -1,87 +0,0 @@
-nextflow.enable.dsl=2
-
-/*
-Testing pipeline for marseq scRNASeq analysis
-*/
-
-include { adaptor_removal} from "./nf_modules/cutadapt/main.nf"
-include {
- index_fasta;
- count;
- index_fasta_velocity;
- count_velocity
-} from "./nf_modules/kb/main.nf" addParams(
- kb_protocol: "marsseq",
- count_out: "quantification/",
- count_velocity_out: "quantification_velocity/"
-)
-
-params.fasta = "http://ftp.ensembl.org/pub/release-94/fasta/gallus_gallus/dna/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa.gz"
-params.fastq = "data/CF42_45/*/*R{1,2}.fastq.gz"
-params.gtf = "http://ftp.ensembl.org/pub/release-94/gtf/gallus_gallus/Gallus_gallus.Gallus_gallus-5.0.94.gtf.gz"
-params.transcript_to_gene = ""
-params.whitelist = "data/expected_whitelist.txt"
-params.config = "data/marseq_flexi_splitter.yaml"
-params.workflow_type = "classic"
-
-log.info "fastq files (--fastq): ${params.fastq}"
-log.info "fasta file (--fasta): ${params.fasta}"
-log.info "gtf file (--gtf): ${params.gtf}"
-log.info "transcript_to_gene file (--transcript_to_gene): ${params.transcript_to_gene}"
-log.info "whitelist file (--whitelist): ${params.whitelist}"
-log.info "config file (--config): ${params.config}"
-
-channel
- .fromFilePairs( params.fastq, size: -1)
- .set { fastq_files }
-channel
- .fromPath( params.fasta )
- .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
- .map { it -> [it.simpleName, it]}
- .set { fasta_files }
-channel
- .fromPath( params.gtf )
- .ifEmpty { error "Cannot find any gtf files matching: ${params.gtf}" }
- .map { it -> [it.simpleName, it]}
- .set { gtf_files }
-if (params.whitelist == "") {
- channel.empty()
- .set { whitelist_files }
-} else {
- channel
- .fromPath( params.whitelist )
- .map { it -> [it.simpleName, it]}
- .set { whitelist_files }
-}
-channel
- .fromPath( params.config )
- .ifEmpty { error "Cannot find any config files matching: ${params.config}" }
- .map { it -> [it.simpleName, it]}
- .set { config_files }
-
-workflow {
- adaptor_removal(fastq_files)
- if (params.workflow_type == "classic") {
- index_fasta(
- fasta_files,
- gtf_files
- )
- count(
- index_fasta.out.index,
- adaptor_removal.out.fastq,
- index_fasta.out.t2g, whitelist_files,config_files
- )
- } else {
- index_fasta_velocity(
- fasta_files,
- gtf_files
- )
- count_velocity(
- index_fasta_velocity.out.index,
- adaptor_removal.out.fastq,
- index_fasta_velocity.out.t2g,
- whitelist_files,
- config_files
- )
- }
-}
diff --git a/src/example_variant_calling.nf b/src/example_variant_calling.nf
deleted file mode 100644
index 5d793ed4..00000000
--- a/src/example_variant_calling.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-nextflow.enable.dsl=2
-
-/*
-Testing pipeline for marseq scRNASeq analysis
-*/
-
-include {
- mapping;
-} from "./nf_modules/bwa/main.nf"
-
-include {
- sort_bam;
-} from "./nf_modules/samtools/main.nf"
-
-include {
- germline_cohort_data_variant_calling;
-} from "./nf_modules/gatk4/main.nf" addParams(
- variant_calling_out: "vcf/",
-)
-
-params.fastq = ""
-params.fasta = ""
-
-channel
- .fromFilePairs( params.fastq, size: -1)
- .set { fastq_files }
-channel
- .fromPath( params.fasta )
- .map { it -> [it.simpleName, it]}
- .set { fasta_files }
-
-workflow {
- mapping(fasta_files, fastq_files)
- sort_bam(mapping.out.bam)
- germline_cohort_data_variant_calling(sort_bam.out.bam, fasta_files)
-}
diff --git a/src/fasta_sampler.nf b/src/fasta_sampler.nf
deleted file mode 100644
index d1200ed4..00000000
--- a/src/fasta_sampler.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-Channel
- .fromPath( "data/tiny_dataset/fasta/*.fasta" )
- .set { fasta_file }
-
-process sample_fasta {
- publishDir "results/sampling/", mode: 'copy'
-
- input:
-file fasta from fasta_file
-
- output:
-file "*_sample.fasta" into fasta_sample
-
- script:
-"""
-head ${fasta} > ${fasta.baseName}_sample.fasta
-"""
-}
diff --git a/src/install_nextflow.sh b/src/install_nextflow.sh
old mode 100755
new mode 100644
diff --git a/src/nextflow b/src/nextflow
new file mode 100644
index 00000000..4a4f0cfd
--- /dev/null
+++ b/src/nextflow
@@ -0,0 +1,465 @@
+#!/usr/bin/env bash
+#
+# Copyright 2020-2021, Seqera Labs
+# Copyright 2013-2019, Centre for Genomic Regulation (CRG)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+[[ "$NXF_DEBUG" == 'x' ]] && set -x
+NXF_VER=${NXF_VER:-'21.04.3'}
+NXF_ORG=${NXF_ORG:-'nextflow-io'}
+NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
+NXF_PROT=${NXF_PROT:-'https'}
+NXF_BASE=${NXF_BASE:-$NXF_PROT://www.nextflow.io/releases}
+NXF_TEMP=${NXF_TEMP:-$TMPDIR}
+NXF_DIST=${NXF_DIST:-$NXF_HOME/framework}
+NXF_CLI="$0 $@"
+
+export NXF_CLI
+export NXF_ORG
+export NXF_HOME
+
+if [[ $TERM && $TERM != 'dumb' ]]; then
+if command -v tput &>/dev/null; then
+GREEN=$(tput setaf 2; tput bold)
+YELLOW=$(tput setaf 3)
+RED=$(tput setaf 1)
+NORMAL=$(tput sgr0)
+fi
+fi
+
+function echo_red() {
+ >&2 echo -e "$RED$*$NORMAL"
+}
+
+function echo_green() {
+ echo -e "$GREEN$*$NORMAL"
+}
+
+function echo_yellow() {
+ >&2 echo -e "$YELLOW$*$NORMAL"
+}
+
+function die() {
+ echo_red "$*"
+ exit 1
+}
+
+function get_abs_filename() {
+ echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
+}
+
+function get() {
+ if command -v curl &>/dev/null; then
+ GET="curl -fsSL '$1' -o '$2'"
+ elif command -v wget &>/dev/null; then
+ GET="wget -q '$1' -O '$2'"
+ else
+ echo_red "ERROR: Cannot find 'curl' nor 'wget' utility -- please install one of them"
+ exit 1
+ fi
+
+ printf "Downloading nextflow dependencies. It may require a few seconds, please wait .. "
+ eval $GET; status=$?
+ printf "\r\033[K"
+ if [ $status -ne 0 ]; then
+ echo_red "ERROR: Cannot download nextflow required file -- make sure you can connect to the internet"
+ echo ""
+ echo "Alternatively you can try to download this file:"
+ echo " $1"
+ echo ""
+ echo "and save it as:"
+ echo " ${3:-$2}"
+ echo ""
+ exit 1
+ fi
+}
+
+function make_temp() {
+ local base=${NXF_TEMP:=$PWD}
+ if [ "$(uname)" = 'Darwin' ]; then mktemp "${base}/nxf-tmp.XXXXXX" || exit $?
+ else mktemp -t nxf-tmp.XXXXXX -p "${base}" || exit $?
+ fi
+}
+
+function resolve_link() {
+ [[ ! -f $1 ]] && exit 1
+ if command -v realpath &>/dev/null; then
+ realpath "$1"
+ elif command -v readlink &>/dev/null; then
+ local target="$1"
+ cd $(dirname $target); target=$(basename $target)
+ while [ -L "$target" ]; do
+ target="$(readlink "$target")"
+ cd $(dirname $target); target=$(basename $target)
+ done
+ echo "$(cd "$(dirname "$target")"; pwd -P)/$target"
+ else
+ echo_yellow "WARN: Neither \`realpath\` nor \`readlink\` command can be found"
+ exit 1
+ fi
+}
+
+function current_ver() {
+ [[ $NXF_EDGE == 1 ]] && printf 'edge' || printf 'latest'
+}
+
+function install() {
+ local tmpfile=$(make_temp)
+ local version=$(set +u; [[ $NXF_VER ]] && printf "v$NXF_VER" || current_ver)
+ local action="a=${2:-default}"
+ get "$NXF_BASE/$version/nextflow?$action" "$tmpfile" "$1" || exit $?
+ mv "$tmpfile" "$1" || exit $?
+ chmod +x "$1" || exit $?
+ bash "$1" -download || exit $?
+ echo ''
+ echo -e $'Nextflow installation completed. Please note:'
+ echo -e $'- the executable file `nextflow` has been created in the folder:' $(dirname $1)
+ if [[ ! "$PATH" =~ (^|:)"$(dirname $1)"(:|$) ]]; then
+ echo -e $'- you may complete the installation by moving it to a directory in your $PATH'
+ fi
+ echo ''
+}
+
+function launch_nextflow() {
+ # the launch command line
+ local cmdline=()
+ # remove leading and trailing double-quotes
+ for x in "${launcher[@]}"; do
+ x="${x%\"}"
+ x="${x#\"}"
+ cmdline+=("$x")
+ done
+
+ if [[ $NXF_MPIRUN ]]; then
+ local rank=''
+ [[ $SLURM_PROCID ]] && rank=$SLURM_PROCID
+ [[ $OMPI_COMM_WORLD_RANK ]] && rank=$OMPI_COMM_WORLD_RANK
+ if [[ ! $rank ]]; then
+ echo_red 'It looks you are not running in a MPI enabled environment -- cannot find `$OMPI_COMM_WORLD_RANK` nor `$SLURM_PROCID` variable';
+ exit 1;
+ fi
+ if [[ $SLURM_CPUS_PER_TASK && $SLURM_MEM_PER_CPU ]]; then
+ export NXF_CLUSTER_MAXCPUS=$SLURM_CPUS_PER_TASK
+ export NXF_CLUSTER_MAXMEMORY="$(($SLURM_MEM_PER_CPU*$SLURM_CPUS_PER_TASK))MB"
+ fi
+ if [[ $rank == 0 ]]; then
+ # sleep a few seconds in order to wait worker daemons to bootstrap
+ sleep ${NXF_SLEEP:-10}
+ export NXF_EXECUTOR='ignite'
+ export NXF_CLUSTER_SHUTDOWNONCOMPLETE='true'
+ else
+ args=(-log .nextflow_node_${rank}.log node ignite)
+ fi
+ # start in daemon mode
+ elif [[ "$bg" ]]; then
+ local pid_file="${NXF_PID_FILE:-.nextflow.pid}"
+ cmdline+=("${args[@]}")
+ exec "${cmdline[@]}" &
+ disown
+ echo $! > "$pid_file"
+ exit 0
+ fi
+
+ cmdline+=("${args[@]}")
+ exec "${cmdline[@]}"
+ exit 1
+}
+
+# check self-install
+if [ "$0" = "bash" ] || [ "$0" = "/bin/bash" ]; then
+ if [ -d nextflow ]; then
+ echo 'Please note:'
+ echo "- The install procedure needs to create a file named 'nextflow' in this folder, but a directory with this name already exists."
+ echo "- Please renamed/delete that directory, or execute the Nextflow install procedure in another folder."
+ echo ''
+ exit 1
+ fi
+ install "$PWD/nextflow" install
+ exit 0
+fi
+
+
+# parse the command line
+bg=''
+dockerize=''
+declare -a jvmopts=()
+declare -a args=("$@")
+declare -a commands=(clone config drop help history info ls pull run view node console kuberun)
+cmd=''
+while [[ $# != 0 ]]; do
+ case $1 in
+ -D*)
+ if [[ ! "$cmd" ]]; then
+ jvmopts+=("$1")
+ fi
+ ;;
+ -d|-dockerize)
+ if [[ ! "$cmd" && ! -f /.nextflow/dockerized ]]; then
+ dockerize=1
+ fi
+ ;;
+ -bg)
+ if [[ ! -f /.nextflow/dockerized ]]; then
+ bg=1
+ fi
+ ;;
+ -download)
+ if [[ ! "$cmd" ]]; then
+ rm -rf "$NXF_DIST/$NXF_VER" || exit $?
+ bash "$0" -version || exit $?
+ exit 0
+ fi
+ ;;
+ -self-update|self-update)
+ if [[ ! "$cmd" ]]; then
+ [[ -z $NXF_EDGE && $NXF_VER = *-edge ]] && NXF_EDGE=1
+ unset NXF_VER
+ install "$0" update
+ exit 0
+ fi
+ ;;
+ -process.executor|-executor.name)
+ if [[ $2 && $2 == 'ignite' ]]; then
+ [ ! $NXF_MODE ] && NXF_MODE='ignite'; shift;
+ fi
+ ;;
+ -with-mpi)
+ [ ! $NXF_MODE ] && NXF_MODE='ignite'
+ NXF_MPIRUN='true'
+ ;;
+ *)
+ [[ $1 && $1 != -* && ! "$cmd" && ${commands[*]} =~ $1 ]] && cmd=$1
+ ;;
+ esac
+ shift
+done
+
+NXF_DOCKER_OPTS=${NXF_DOCKER_OPTS:=''}
+if [[ "$dockerize" ]]; then
+ if [[ "$bg" ]]; then detach='--detach '; else detach=''; fi
+ NXF_ASSETS=${NXF_ASSETS:-${NXF_HOME:-$HOME/.nextflow}/assets}
+ mkdir -p "$NXF_ASSETS"
+ exec docker run $detach --rm --net host \
+ -e NXF_ANSI_LOG=false \
+ -e USER -e HOME -e NXF_ASSETS=$NXF_ASSETS -e NXF_USRMAP=$(id -u) -e NXF_DOCKER_OPTS='-u $(id -u)' \
+ -v /var/run/docker.sock:/var/run/docker.sock \
+ -v $HOME:$HOME:ro,Z -v $NXF_ASSETS:$NXF_ASSETS:Z -v $PWD:$PWD:Z -w $PWD $NXF_DOCKER_OPTS \
+ nextflow/nextflow:$NXF_VER nextflow "${args[@]}"
+ exit 1
+fi
+
+CAPSULE_LOG=${CAPSULE_LOG:=''}
+CAPSULE_RESET=${CAPSULE_RESET:=''}
+CAPSULE_CACHE_DIR=${CAPSULE_CACHE_DIR:="$NXF_HOME/capsule"}
+
+NXF_PACK=one
+NXF_MODE=${NXF_MODE:-''}
+NXF_JAR=${NXF_JAR:-nextflow-$NXF_VER-$NXF_PACK.jar}
+NXF_BIN=${NXF_BIN:-$NXF_DIST/$NXF_VER/$NXF_JAR}
+NXF_PATH=$(dirname "$NXF_BIN")
+NXF_URL=${NXF_URL:-$NXF_BASE/v$NXF_VER/$NXF_JAR}
+NXF_GRAB=${NXF_GRAB:-''}
+NXF_CLASSPATH=${NXF_CLASSPATH:-''}
+NXF_MPIRUN=${NXF_MPIRUN:=''}
+NXF_HOST=${HOSTNAME:-localhost}
+[[ $NXF_LAUNCHER ]] || NXF_LAUNCHER=${NXF_HOME}/tmp/launcher/nextflow-${NXF_PACK}_${NXF_VER}/${NXF_HOST}
+
+if [[ $NXF_MODE == ignite ]]; then
+ # Fix JDK bug when there's a limit on the OS virtual memory
+ # https://bugs.openjdk.java.net/browse/JDK-8044054
+ # https://issues.apache.org/jira/browse/HADOOP-7154
+ export MALLOC_ARENA_MAX=4
+fi
+
+# Determine the path to this file
+if [[ $NXF_PACK = all ]]; then
+ NXF_BIN=$(which "$0" 2>/dev/null)
+ [ $? -gt 0 -a -f "$0" ] && NXF_BIN="./$0"
+fi
+
+# use nextflow custom java home path
+if [[ "$NXF_JAVA_HOME" ]]; then
+ JAVA_HOME="$NXF_JAVA_HOME"
+ unset JAVA_CMD
+fi
+# Determine the Java command to use to start the JVM.
+if [ ! -x "$JAVA_CMD" ] ; then
+ if [ -d "$JAVA_HOME" ] ; then
+ if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+ # IBM's JDK on AIX uses strange locations for the executables
+ JAVA_CMD="$JAVA_HOME/jre/sh/java"
+ else
+ JAVA_CMD="$JAVA_HOME/bin/java"
+ fi
+ elif [ -x /usr/libexec/java_home ]; then
+ JAVA_CMD="$(/usr/libexec/java_home -v 1.8+)/bin/java"
+ else
+ JAVA_CMD="$(which java)" || JAVA_CMD=java
+ fi
+fi
+
+# Retrieve the java version from a NF local file
+JAVA_KEY="$NXF_HOME/tmp/ver/$(resolve_link "$JAVA_CMD" | sed 's@/@.@g')"
+if [ -f "$JAVA_KEY" ]; then
+ JAVA_VER="$(cat "$JAVA_KEY")"
+else
+ JAVA_VER="$("$JAVA_CMD" $NXF_OPTS -version 2>&1)"
+ if [ $? -ne 0 ]; then
+ echo_red "${JAVA_VER:-Failed to launch the Java virtual machine}"
+ echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_OPTS: $NXF_OPTS\n"
+ exit 1
+ fi
+ JAVA_VER=$(echo "$JAVA_VER" | awk '/version/ {gsub(/"/, "", $3); print $3}')
+ # check NF version
+ if [[ ! $NXF_VER =~ ([0-9]+)\.([0-9]+)\.([0-9].*) ]]; then
+ echo_red "Not a valid Nextflow version: $NXF_VER"
+ exit 1
+ fi
+ major=${BASH_REMATCH[1]}
+ minor=${BASH_REMATCH[2]}
+ # legacy version - Java 7/8 only
+ if [ $major -eq 0 ] && [ $minor -lt 26 ]; then
+ version_check="^(1.7|1.8)"
+ version_message="Java 7 or 8"
+ else
+ version_check="^(1.8|9|10|11|12|13|14|15)"
+ version_message="Java 8 or later"
+ fi
+ if [[ ! $JAVA_VER =~ $version_check ]]; then
+ echo_red "ERROR: Cannot find Java or it's a wrong version -- please make sure that $version_message is installed"
+ if [[ "$NXF_JAVA_HOME" ]]; then
+ echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_JAVA_HOME: $NXF_JAVA_HOME\n"
+ else
+ echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n JAVA_HOME: $JAVA_HOME\n"
+ fi
+ exit 1
+ fi
+ if [[ ! $JAVA_VER =~ ^(1.8|9|10|11|12|13|14|15) ]]; then
+ echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 8 up to 15\n"
+ elif [[ ! $JAVA_VER =~ ^(1.8|9|10|11) && $NXF_MODE == ignite ]]; then
+ echo_yellow "WARN: Apache Ignite executor is not tested with Java $JAVA_VER -- It's recommended the use of version 8 up to 11\n"
+ fi
+ mkdir -p $(dirname "$JAVA_KEY")
+ [[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY"
+fi
+
+# Verify nextflow jar is available
+if [ ! -f "$NXF_BIN" ]; then
+ [ -f "$NXF_PATH" ] && rm "$NXF_PATH"
+ mkdir -p "$NXF_PATH" || exit $?
+ tmpfile=$(make_temp)
+ get "$NXF_URL" "$tmpfile" "$NXF_BIN"
+ mv "$tmpfile" "$NXF_BIN"
+fi
+
+COLUMNS=${COLUMNS:-`tty -s && tput cols 2>/dev/null || true`}
+declare -a JAVA_OPTS=()
+JAVA_OPTS+=(-Dfile.encoding=UTF-8 -Dcapsule.trampoline -Dcapsule.java.cmd="$JAVA_CMD")
+if [[ $cmd == console ]]; then bg=1;
+else JAVA_OPTS+=(-Djava.awt.headless=true)
+fi
+
+[[ "$JAVA_HOME" ]] && JAVA_OPTS+=(-Dcapsule.java.home="$JAVA_HOME")
+[[ "$CAPSULE_LOG" ]] && JAVA_OPTS+=(-Dcapsule.log=$CAPSULE_LOG)
+[[ "$CAPSULE_RESET" ]] && JAVA_OPTS+=(-Dcapsule.reset=true)
+[[ "$cmd" != "run" && "$cmd" != "node" ]] && JAVA_OPTS+=(-XX:+TieredCompilation -XX:TieredStopAtLevel=1)
+[[ "$NXF_OPTS" ]] && JAVA_OPTS+=($NXF_OPTS)
+[[ "$NXF_CLASSPATH" ]] && export NXF_CLASSPATH
+[[ "$NXF_GRAB" ]] && export NXF_GRAB
+[[ "$COLUMNS" ]] && export COLUMNS
+[[ "$NXF_TEMP" ]] && JAVA_OPTS+=(-Djava.io.tmpdir="$NXF_TEMP")
+[[ "${jvmopts[@]}" ]] && JAVA_OPTS+=("${jvmopts[@]}")
+export JAVA_CMD
+export CAPSULE_CACHE_DIR
+export NXF_PLUGINS_DIR
+export NXF_PLUGINS_MODE
+export NXF_PLUGINS_DEFAULT
+export NXF_PACK
+
+# lookup the a `md5` command
+if hash md5sum 2>/dev/null; then MD5=md5sum;
+elif hash gmd5sum 2>/dev/null; then MD5=gmd5sum;
+elif hash md5 2>/dev/null; then MD5=md5;
+else MD5=''
+fi
+
+# when no md5 command is available fallback on default execution
+if [ ! "$MD5" ] || [ "$CAPSULE_RESET" ]; then
+ launcher=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
+ launch_nextflow
+ exit 1
+fi
+
+# creates a md5 unique for the given variables
+env_md5() {
+cat <<EOF | $MD5 | cut -f1 -d' '
+$JAVA_CMD
+$JAVA_VER
+${JAVA_OPTS[@]}
+$NXF_HOME
+$NXF_VER
+$NXF_OPTS
+$NXF_GRAB
+$NXF_CLASSPATH
+EOF
+}
+
+# checked if a cached classpath file exists and it newer that the nextflow boot jar file
+if [[ -f /.nextflow/dockerized ]]; then
+ LAUNCH_FILE=/.nextflow/launch-classpath
+else
+ LAUNCH_FILE="${NXF_LAUNCHER}/classpath-$(env_md5)"
+fi
+if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ]; then
+ launcher=($(cat "$LAUNCH_FILE"))
+else
+ # otherwise run the capsule and get the result classpath in the 'launcher' and save it to a file
+ cli=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
+ [[ $? -ne 0 ]] && echo_red 'Unable to initialize nextflow environment' && exit 1
+
+ if [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15) ]]; then
+ launcher=("${cli[@]:0:1}")
+ launcher+=(--add-opens=java.base/java.lang=ALL-UNNAMED)
+ launcher+=(--add-opens=java.base/java.io=ALL-UNNAMED)
+ launcher+=(--add-opens=java.base/java.nio=ALL-UNNAMED)
+ launcher+=(--add-opens=java.base/java.util=ALL-UNNAMED)
+ launcher+=(--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED)
+ launcher+=(--add-opens=java.base/sun.nio.ch=ALL-UNNAMED)
+ launcher+=(--add-opens=java.base/sun.nio.fs=ALL-UNNAMED)
+ launcher+=(--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED)
+ launcher+=(--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED)
+ launcher+=(--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED)
+ launcher+=(--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED)
+ launcher+=(--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED)
+ launcher+=(--illegal-access=deny)
+ launcher+=("${cli[@]:1}")
+ else
+ launcher=("${cli[@]}")
+ fi
+
+ # Don't show errors if the LAUNCH_FILE can't be created
+ if mkdir -p "${NXF_LAUNCHER}" 2>/dev/null; then
+ STR=''
+ for x in "${launcher[@]}"; do
+ [[ "$x" != "\"-Duser.dir=$PWD\"" ]] && STR+="$x "
+ done
+ printf "$STR">"$LAUNCH_FILE"
+ else
+ echo_yellow "Warning: Couldn't create cached classpath folder: $NXF_LAUNCHER -- Maybe NXF_HOME is not writable?"
+ fi
+
+fi
+
+# finally run it
+launch_nextflow
diff --git a/src/nextflow.config b/src/nextflow.config
index 05a44103..ffe70eb3 100644
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -18,7 +18,6 @@ profiles {
docker.enabled = true
process {
errorStrategy = 'finish'
- memory = '16GB'
withLabel: big_mem_mono_cpus {
cpus = 1
}
@@ -40,7 +39,6 @@ profiles {
singularity.cacheDir = "./bin/"
process {
errorStrategy = 'finish'
- memory = '16GB'
withLabel: big_mem_mono_cpus {
cpus = 1
}
diff --git a/src/nf_functions/control_ip_processing.nf b/src/nf_functions/control_ip_processing.nf
new file mode 100644
index 00000000..6f0fd325
--- /dev/null
+++ b/src/nf_functions/control_ip_processing.nf
@@ -0,0 +1,24 @@
+bam_files_control = Channel.create()
+bam_files_ip = Channel.create()
+sorted_bam_files_macs2
+ .map {
+ file ->
+ def file_name = file[1].name.toString()
+ def key = (file_name =~ /(.+)\_[^_]+\_sorted\.bam/)[0][1]
+ return tuple(key, file)
+ }
+ .groupTuple()
+ .map{
+ file_list ->
+ def input_list = [file_list[0]]
+ def ip_list = []
+ for (files in file_list[1]) {
+ if (files[0] =~ /.*${params.control_tag}.*/) {
+ input_list.add(files[1])
+ } else {
+ ip_list.add(files[1])
+ }
+ }
+ return [input_list, ip_list]
+ }
+ .separate( bam_files_control, bam_files_ip){a -> [a[0], a[1]]}
\ No newline at end of file
diff --git a/src/nf_functions/reads_processing.nf b/src/nf_functions/reads_processing.nf
new file mode 100644
index 00000000..35fb2b28
--- /dev/null
+++ b/src/nf_functions/reads_processing.nf
@@ -0,0 +1,5 @@
+def merge_channels(report1, report2) {
+
+ return report1.concat(report2).collect()
+
+}
\ No newline at end of file
diff --git a/src/nf_modules/multiqc/main.nf b/src/nf_modules/multiqc/main.nf
index f33386d2..faf4c6d9 100644
--- a/src/nf_modules/multiqc/main.nf
+++ b/src/nf_modules/multiqc/main.nf
@@ -5,7 +5,7 @@
/*
include { multiqc }
- from './nf_modules/multiqc/main'
+ from './nf_modules/multiqc/main.nf'
addParams(
multiqc_out: "QC/"
)
diff --git a/src/solution_RNASeq.nf b/src/solution_RNASeq.nf
deleted file mode 100644
index 23adf099..00000000
--- a/src/solution_RNASeq.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-nextflow.enable.dsl=2
-
-include { fastp } from "./nf_modules/fastp/main.nf"
-include { fasta_from_bed } from "./nf_modules/bedtools/main.nf"
-include { index_fasta; mapping_fastq } from './nf_modules/kallisto/main.nf' addParams(mapping_fastq_out: "quantification/")
-
-
-params.fastq = "data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files: ${params.fastq}"
-log.info "fasta file : ${params.fasta}"
-log.info "bed file : ${params.bed}"
-
-channel
- .fromFilePairs( params.fastq, size: -1)
- .set { fastq_files }
-
-channel
- .fromPath( params.fasta )
- .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
- .map { it -> [it.simpleName, it]}
- .set { fasta_files }
-channel
- .fromPath( params.bed )
- .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
- .map { it -> [it.simpleName, it]}
- .set { bed_files }
-
-workflow {
- fastp(fastq_files)
- fasta_from_bed(fasta_files, bed_files)
- index_fasta(fasta_from_bed.out.fasta)
- mapping_fastq(index_fasta.out.index.collect(), fastp.out.fastq)
-}
diff --git a/src/training_dataset.config b/src/training_dataset.config
deleted file mode 100644
index 734a7410..00000000
--- a/src/training_dataset.config
+++ /dev/null
@@ -1,370 +0,0 @@
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- withName: build_synthetic_bed {
- container = "lbmc/bedtools:2.25.0"
- cpus = 1
- }
- withName: fasta_from_bed {
- container = "lbmc/bedtools:2.25.0"
- cpus = 1
- }
- withName: index_fasta {
- container = "lbmc/bowtie2:2.3.4.1"
- cpus = 4
- }
- withName: mapping_fastq_paired {
- container = "lbmc/bowtie2:2.3.4.1"
- cpus = 4
- }
- withName: bam_2_fastq_paired {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: filter_bam_paired {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: sort_bam_paired {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: index_bam_paired {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: mapping_fastq_single {
- container = "lbmc/bowtie2:2.3.4.1"
- cpus = 4
- }
- withName: bam_2_fastq_single {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: filter_bam_single {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: sort_bam_single {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: index_bam_single {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- process {
- withName: build_synthetic_bed {
- container = "lbmc/bedtools:2.25.0"
- cpus = 1
- }
- withName: fasta_from_bed {
- container = "lbmc/bedtools:2.25.0"
- cpus = 1
- }
- withName: index_fasta {
- container = "lbmc/bowtie2:2.3.4.1"
- cpus = 4
- }
- withName: mapping_fastq_single {
- container = "lbmc/bowtie2:2.3.4.1"
- cpus = 4
- }
- withName: mapping_fastq_paired {
- container = "lbmc/bowtie2:2.3.4.1"
- cpus = 4
- }
- withName: bam_2_fastq_paired {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: filter_bam_paired {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: sort_bam_paired {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: index_bam_paired {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: bam_2_fastq_single {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: filter_bam_single {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: sort_bam_single {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- withName: index_bam_single {
- container = "lbmc/samtools:1.7"
- cpus = 4
- }
- }
- }
- psmn {
- process{
- withName: build_synthetic_bed {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bedtools_2.25.0"
- executor = "sge"
- clusterOptions = "-m e -cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- withName: fasta_from_bed {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bedtools_2.25.0"
- executor = "sge"
- clusterOptions = "-m e -cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = "monointeldeb128"
- }
- withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
- executor = "sge"
- clusterOptions = "-m e -cwd -V"
- cpus = 32
- memory = "20GB"
- time = "12h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- withName: mapping_fastq_paired {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
- executor = "sge"
- clusterOptions = "-m e -cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- withName: bam_2_fastq_paired {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
- executor = "sge"
- clusterOptions = "-m e -cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- withName: sort_bam_paired {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
- executor = "sge"
- clusterOptions = "-m e -cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- withName: index_bam_paired {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
- executor = "sge"
- clusterOptions = "-m e -cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- withName: mapping_fastq_single {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
- executor = "sge"
- clusterOptions = "-m e -cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- withName: bam_2_fastq_single {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
- executor = "sge"
- clusterOptions = "-m e -cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- withName: sort_bam_single {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
- executor = "sge"
- clusterOptions = "-m e -cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- withName: index_bam_single {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
- executor = "sge"
- clusterOptions = "-m e -cwd -V"
- cpus = 32
- memory = "30GB"
- time = "24h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
- penv = "openmp32"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
- process{
- withName: fasta_from_bed {
- container = "lbmc/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"
- }
- }
- process{
- withName: build_synthetic_bed {
- container = "lbmc/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"
- }
- withName: fasta_from_bed {
- container = "lbmc/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"
- }
- withName: index_fasta {
- container = "lbmc/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"
- }
- withName: mapping_fastq_paired {
- container = "lbmc/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"
- }
- withName: bam_2_fastq_paired {
- container = "lbmc/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: sort_bam_paired {
- container = "lbmc/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: index_bam_paired {
- container = "lbmc/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: mapping_fastq_single {
- container = "lbmc/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"
- }
- withName: bam_2_fastq_single {
- container = "lbmc/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: sort_bam_single {
- container = "lbmc/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: index_bam_single {
- container = "lbmc/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"
- }
- }
- }
-}
diff --git a/src/training_dataset.nf b/src/training_dataset.nf
deleted file mode 100644
index c6f48e88..00000000
--- a/src/training_dataset.nf
+++ /dev/null
@@ -1,308 +0,0 @@
-/*
-small pipeline to build a training dataset from whole genome data
-
-input:
-- fasta
-- fastq
-- chromosome
-- start position
-- stop position
-
-output:
-- sort fasta
-- sort fastq
-
-example for paired-end data:
-./nextflow src/training_dataset.nf -c src/training_dataset.config --fasta "data/genome.fa" --fastq_paired "data/*_R{1,2}.fastq.gz" --chromosome "X" --start 5305683 --stop 5333928 -resume
-
-example for single-end data:
-./nextflow src/training_dataset.nf -c src/training_dataset.config --fasta "data/genome.fa" --fastq_single "data/*_R1.fastq.gz" --chromosome "X" --start 5305683 --stop 5333928 -resume
-
-*/
-
-params.fastq_paired = ""
-params.fastq_single = ""
-
-log.info "fasta files : ${params.fasta}"
-log.info "fastq paired files : ${params.fastq_paired}"
-log.info "fastq single files : ${params.fastq_single}"
-log.info "chromosome : ${params.chromosome}"
-log.info "start position : ${params.start}"
-log.info "stop position : ${params.stop}"
-
-
-Channel
- .fromPath( params.fasta )
- .ifEmpty { error "Cannot find any index files matching: ${params.fasta}" }
- .set { fasta_file }
-
-
-process build_synthetic_bed {
- tag "${chromosome}:${start}-${stop}"
- cpus 4
-
- input:
- val chromosome from params.chromosome
- val start from params.start
- val stop from params.stop
-
- output:
- file "*.bed" into bed_files
-
- script:
-"""
-echo "${chromosome}\t${start}\t${stop}" > synthetic.bed
-"""
-}
-
-process fasta_from_bed {
- tag "${fasta.baseName}"
- cpus 4
- publishDir "results/training/fasta/", mode: 'copy'
-
- input:
- file fasta from fasta_file
- file bed from bed_files
- val chromosome from params.chromosome
-
- output:
- file "*.fasta" into fasta_files_extracted
-
- script:
-"""
-bedtools getfasta \
--fi ${fasta} -bed ${bed} -fo s${fasta.baseName}.fasta
-"""
-}
-
-process index_fasta {
- tag "$fasta.baseName"
- cpus 4
- publishDir "results/training/mapping/index/", mode: 'copy'
-
- input:
- file fasta from fasta_files_extracted
-
- output:
- file "*.index*" into index_files
- file "*_report.txt" into indexing_report
-
- script:
-"""
-bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
-
-if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
- exit 1
-fi
-"""
-}
-
-if ( params.fastq_paired != "" ) {
- Channel
- .fromFilePairs( params.fastq_paired )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq_paired}" }
- .set { fastq_files_paired }
-
- process mapping_fastq_paired {
- tag "$pair_id"
- cpus 4
-
- input:
- set pair_id, file(reads) from fastq_files_paired
- file index from index_files.collect()
-
- output:
- set pair_id, "*.bam" into bam_files_paired
- file "*_report.txt" into mapping_report
-
- script:
- index_id = index[0]
- for (index_file in index) {
- if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
- index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
- }
- }
- """
- bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
- -1 ${reads[0]} -2 ${reads[1]} 2> \
- ${pair_id}_bowtie2_report.txt | \
- samtools view -Sb - > ${pair_id}.bam
-
- if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
- exit 1
- fi
- """
- }
-
- bam_files_paired.into{ bam_files_paired_fa; bam_files_paired_ba}
-
- process bam_2_fastq_paired {
- tag "$file_id"
- publishDir "results/training/fastq/", mode: 'copy'
-
- input:
- set file_id, file(bam) from bam_files_paired_fa
-
- output:
- set file_id, "*.fastq" into fastq_files_extracted
- script:
- """
- samtools fastq -1 s${file_id}_R1.fastq -2 s${file_id}_R2.fastq -F 0x4 ${bam}
- """
- }
-
- process filter_bam_paired {
- tag "$file_id"
- cpus 4
-
- input:
- set file_id, file(bam) from bam_files_paired_ba
- file bed from bed_files
-
- output:
- set file_id, "*.bam" into filtered_bam_files_paired
- script:
- """
- samtools view -@ ${task.cpus} -hb ${bam} -F 0x4 > f${file_id}.bam
- """
- }
-
- process sort_bam_paired {
- tag "$file_id"
- publishDir "results/training/bams/", mode: 'copy'
- cpus 4
-
- input:
- set file_id, file(bam) from filtered_bam_files_paired
-
- output:
- set file_id, "*.bam" into sorted_bam_files_paired
-
- script:
- """
- samtools sort -@ ${task.cpus} -O BAM -o s${file_id}.bam ${bam}
- """
- }
-
- process index_bam_paired {
- tag "$file_id"
- publishDir "results/training/bams/", mode: 'copy'
-
- input:
- set file_id, file(bam) from sorted_bam_files_paired
-
- output:
- set file_id, "*.bam*" into indexed_bam_file_paired
-
- script:
- """
- samtools index ${bam}
- """
- }
-}
-
-
-if ( params.fastq_single != "" ) {
- Channel
- .fromPath( params.fastq_single )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq_single}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { fastq_files_single }
-
- process mapping_fastq_single {
- tag "$file_id"
- cpus 4
-
- input:
- set file_id, file(reads) from fastq_files_single
- file index from index_files.collect()
-
- output:
- set file_id, "*.bam" into bam_files_single
- file "*_report.txt" into mapping_report
-
- script:
- index_id = index[0]
- for (index_file in index) {
- if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
- index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
- }
- }
- """
- bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
- -U ${reads} 2> \
- ${file_id}_bowtie2_report.txt | \
- samtools view -Sb - > ${file_id}.bam
-
- if grep -q "Error" ${file_id}_bowtie2_report.txt; then
- exit 1
- fi
- """
- }
-
- bam_files_single.into{ bam_files_single_fa; bam_files_single_ba}
-
- process bam_2_fastq_single {
- tag "$file_id"
-
- input:
- set file_id, file(bam) from bam_files_single_fa
-
- output:
- set file_id, "*.fastq" into fastq_files_extracted
- script:
- """
- samtools fastq -0 s${file_id}.fastq -F 0x4 ${bam}
- """
- }
-
- process filter_bam_single {
- tag "$file_id"
- cpus 4
-
- input:
- set file_id, file(bam) from bam_files_single_ba
- file bed from bed_files
-
- output:
- set file_id, "*.bam" into filtered_bam_files_single
- script:
- """
- samtools view -@ ${task.cpus} -hb ${bam} -F 0x4 > f${file_id}.bam
- """
- }
-
- process sort_bam_single {
- tag "$file_id"
- publishDir "results/training/bams/", mode: 'copy'
- cpus 4
-
- input:
- set file_id, file(bam) from filtered_bam_files_single
-
- output:
- set file_id, "*.bam" into sorted_bam_files_single
-
- script:
- """
- samtools sort -@ ${task.cpus} -O BAM -o s${file_id}.bam ${bam}
- """
- }
-
- process index_bam_single {
- tag "$file_id"
- publishDir "results/training/bams/", mode: 'copy'
-
- input:
- set file_id, file(bam) from sorted_bam_files_single
-
- output:
- set file_id, "*.bam*" into indexed_bam_file_single
-
- script:
- """
- samtools index ${bam}
- """
- }
-}
-
--
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