diff --git a/src/conda_psmn.sh b/src/conda_psmn.sh
new file mode 100644
index 0000000000000000000000000000000000000000..3a91a796363fdad29014c4df79874754b9b2621a
--- /dev/null
+++ b/src/conda_psmn.sh
@@ -0,0 +1,5 @@
+#!/bin/sh
+CONDA_PATH=/Xnfs/lbmcdb/common/conda/
+source ${CONDA_PATH}init.sh
+CONDA_ENVS=${CONDA_PATH}/envs/
+
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index aa59cf49a1fe9b6e656e3f00be78104488138fb7..574e6d730d097c14c6f690aca8d8bb83373373a7 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "bedtools_2.25.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 91a0fc567e3161c0102f61bdf3b23f75b7d14629..4b554a7bada09952e5b1c9bd26ebd5c09c09ea62 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_fasta {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "bowtie/1.2.2"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "bowtie_1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index d33ae6c6704b0b954192a55ff0a3c89b1b3affda..49eb9c53791cc79c0942f8979ca93a57348d20d4 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -22,8 +22,8 @@ profiles {
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 = "./src/conda_psmn.sh"
+ conda = "bowtie/1.2.2:samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index d33ae6c6704b0b954192a55ff0a3c89b1b3affda..49eb9c53791cc79c0942f8979ca93a57348d20d4 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -22,8 +22,8 @@ profiles {
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 = "./src/conda_psmn.sh"
+ conda = "bowtie/1.2.2:samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 8c5742cfaf6aa8f62df57f329ea753a50f353439..5ed9bcc390d5de7a367de78e285c537d76b5c7dc 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index a5c9b8275bedff97407ca649df29fb55dc8fbb29..bc1c8979a4b1bd7912be6310bcf79e7ea2c2be4e 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index a5c9b8275bedff97407ca649df29fb55dc8fbb29..bc1c8979a4b1bd7912be6310bcf79e7ea2c2be4e 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index a8e7a27e8f948af09c793f91b6d1ff19f6775886..4e89c3be04dd9e3ed81c685fce928bfcaac2a3f8 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "bwa_0.7.17"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index b0a49229d928c0cacb22750913416a135bada978..aebe28c5b07a34c6637e870761b8e28722f14fab 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "bwa_0.7.17"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 2dd2681e93c4d0190ecc3166c8a4d555fc1e065b..8e62c1cc9cef35b46d88659056f2a033206f7c90 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: adaptor_removal {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "cutadapt/2.1"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 2dd2681e93c4d0190ecc3166c8a4d555fc1e065b..8e62c1cc9cef35b46d88659056f2a033206f7c90 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: adaptor_removal {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "cutadapt/2.1"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 2c8c65a1ab9810cc76cbacbe473df7ed5901eace..f94b4e4822dc58128e8659a5ef3dd625ca2171fe 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: trimming {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "cutadapt/2.1"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 2c8c65a1ab9810cc76cbacbe473df7ed5901eace..f94b4e4822dc58128e8659a5ef3dd625ca2171fe 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: trimming {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "cutadapt/2.1"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 720561761b5a86ad3621715d33c39fc30f4994f6..13952d879c66d04353c679d1bd894b5f5130434c 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -30,8 +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 = "./src/conda_psmn.sh"
+ conda = "sambamba_0.6.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 3eb067b5b3fd784d360a7eb260624fd412105151..ea4bab25f53e1fb14c55fd6e20803bd335547299 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "deeptools_3.0.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 7068f94cc72eec6ce5d58091f70c107811df4ca3..184835474200415f46cc563a906c1bc89de23ce2 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "deeptools_3.0.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index c2fcafa50122098aaa954a9035fc265293e2cdff..6cece587f1332d33e95da86bb2772cfc2a1ef61f 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastp_fastq {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "fastp/0.19.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "fastp_0.19.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index c2fcafa50122098aaa954a9035fc265293e2cdff..6cece587f1332d33e95da86bb2772cfc2a1ef61f 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastp_fastq {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "fastp/0.19.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "fastp_0.19.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 75d352bc541fcfe51bff9ffdf4a7aa480a42cd58..6731be65d1cda3525b93163fa4084914c8cf8f0d 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastqc_fastq {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "fastqc/0.11.5"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "fastqc_0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 75d352bc541fcfe51bff9ffdf4a7aa480a42cd58..6731be65d1cda3525b93163fa4084914c8cf8f0d 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastqc_fastq {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "fastqc/0.11.5"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "fastqc_0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index 80cf1ea07350ed7befe6be965b424a1088d99f49..01646ee1a4a38a6a80171e0fc97527162f89919d 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_fasta {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "hisat2/2.1.0"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "hisat2_2.1.0"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index cc6255c246351edf8a97d9b0ea05cc788a9b6cf2..8d1d44724f1d5b8edef967afa63c3222327f4a22 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -30,8 +30,8 @@ profiles {
psmn{
process{
withName: sort_bam {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index d5783a2b0b4bd3e3be4e296b8a11acd4b95dc55f..8a038dd9bb069866ff152f05950ff45f889be6a7 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "kallisto_0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 175b0f9245a98f55eb1aa08d86601e229b4afb9c..8ac5af00c53b74646bf0d320b50e3f2a9b72f0e7 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "kallisto_0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 175b0f9245a98f55eb1aa08d86601e229b4afb9c..8ac5af00c53b74646bf0d320b50e3f2a9b72f0e7 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "kallisto_0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index ef11303d8a2dc634668f2f8cf557f0b0630a29f6..d9a72019ae48fe8c16bb4a41d6ec1715d27c4199 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "macs2_2.1.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 295a824d3c6ec97b49db85dcbd0f1f46f77bdcd8..40754658a5d749d4d88aee2d286b0672809b3dde 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -31,8 +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 = "./src/conda_psmn.sh"
+ conda = "fastqc_0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index f43250944db66a534dbf604d90b6f80af366d667..f440d1463b8d6a5c04523f6a78fb31cc1b6ae291 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -30,8 +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 = "./src/conda_psmn.sh"
+ conda = "fastqc_0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 8d00ba922ee6420eb94691b1a6fc0b9ad5a186a8..d0841719696253cc65bd4ee614e144e7642674b3 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -38,8 +38,8 @@ profiles {
psmn{
process{
withName: compute_mappability {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "music/6613c53"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "music_6613c53"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index 0b40f13bdbb192a4294d8380ed441df03283ce7f..d49f444a40326f18c6559e3de0a9a7364135cc03 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "rsem_1.3.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 15bdaa8a9c950e20ad2ba2b4833a051517ecb431..90eaae7075dc36b2a4a56371edf0968dda903044 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "rsem_1.3.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 15bdaa8a9c950e20ad2ba2b4833a051517ecb431..90eaae7075dc36b2a4a56371edf0968dda903044 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "rsem_1.3.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 7d19d20b56e4c35d628ffefe5bc248d0300f2da8..d1dd2c3ad3b93d85ebf87ce9cd18f581c41c3eda 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "sambamba_0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index c77b4b322d9f610101bd2876b64ae8a2e3f4c8ca..145fa48d189c0087aceb8d98bfe332f29a6d7ff5 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "sambamba_0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 4
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index b37dade1565062bf719c3bded5081e660889c495..afd305f9b4d7ed52d2ad5d3e459da0a3793bd3d3 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "sambamba_0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 08a0a6330cd95d57980f063197c2ad5a615d9276..0b4f093b1404216f0c6112684860f47d7c3bc14b 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "samblaster_0.1.24"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 06a63e48ea78bb5ad53eecaffc77228cf8c77afc..69f9664feb4634b3a1a8d229fb194d5f5212e5d2 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: filter_bam {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 09e97bb49b792c4301756b5b311b4bcfeb07177f..49bc53f8909f871beb3db423eca8854daaee4c5a 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_bam {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 0cb3bf1f9f91dc93b77fb168c7ac4c5fc6c95a68..8436342a6055c5a1490898971a5f6886afa550ec 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: sort_bam {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 34523d0f72934799a6fde17934045249f856cfcd..eb4468d9f018e356b79a420fd2c2127ce09908e5 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: split_bam {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 9e6bd1986d32489d78f75243932f2595319bb179..ad33eec91395933e1fc94591957bd8ed8f60e4a8 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -22,8 +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 = "./src/conda_psmn.sh"
+ conda = "sratoolkit_2.8.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index d08b7b8573db3816598afc421ec90d66d6394ab9..4e8e0340007d862dfb34c64da5db853bd8364bf1 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -30,8 +30,8 @@ profiles {
psmn{
process{
withName: sort_bam {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 3f09a7e5f54111e0815cfc9426b750fd76d02a8d..ccc103111df879be9112a2068f2bb86a3b38ccc9 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: trimming {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "urqt/d62c1f8"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "urqt_d62c1f8"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "5GB"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 0d2254d56721461a62ef1f91b1851cd6359e4e8c..a9806cebc95c8701ebb4d137178e12384b2a4e44 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: trimming {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "urqt/d62c1f8"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "urqt_d62c1f8"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16