From e58b21b6dfdd8991189d095a189184bcc0b05867 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 6 Nov 2019 16:05:50 +0100
Subject: [PATCH] nf: change psmn config to use conda
---
src/conda_psmn.sh | 5 +++++
src/nf_modules/bedtools/fasta_from_bed.config | 4 ++--
src/nf_modules/bowtie/indexing.config | 4 ++--
src/nf_modules/bowtie/mapping_paired.config | 4 ++--
src/nf_modules/bowtie/mapping_single.config | 4 ++--
src/nf_modules/bowtie2/indexing.config | 4 ++--
src/nf_modules/bowtie2/mapping_paired.config | 4 ++--
src/nf_modules/bowtie2/mapping_single.config | 4 ++--
src/nf_modules/bwa/indexing.config | 4 ++--
src/nf_modules/bwa/mapping_paired.config | 4 ++--
src/nf_modules/cutadapt/adaptor_removal_paired.config | 4 ++--
src/nf_modules/cutadapt/adaptor_removal_single.config | 4 ++--
src/nf_modules/cutadapt/trimming_paired.config | 4 ++--
src/nf_modules/cutadapt/trimming_single.config | 4 ++--
src/nf_modules/deeptools/bam_to_bigwig.config | 4 ++--
src/nf_modules/deeptools/compute_matrix.config | 4 ++--
src/nf_modules/deeptools/plot_profile.config | 4 ++--
src/nf_modules/fastp/fastp_paired.config | 4 ++--
src/nf_modules/fastp/fastp_single.config | 4 ++--
src/nf_modules/fastqc/fastqc_paired.config | 4 ++--
src/nf_modules/fastqc/fastqc_single.config | 4 ++--
src/nf_modules/hisat2/indexing.config | 4 ++--
src/nf_modules/htseq/htseq.config | 4 ++--
src/nf_modules/kallisto/indexing.config | 4 ++--
src/nf_modules/kallisto/mapping_paired.config | 4 ++--
src/nf_modules/kallisto/mapping_single.config | 4 ++--
src/nf_modules/macs2/peak_calling.config | 4 ++--
src/nf_modules/multiqc/multiqc_paired.config | 4 ++--
src/nf_modules/multiqc/multiqc_single.config | 4 ++--
src/nf_modules/music/peak_calling_single.config | 4 ++--
src/nf_modules/rsem/indexing.config | 4 ++--
src/nf_modules/rsem/quantification_paired.config | 4 ++--
src/nf_modules/rsem/quantification_single.config | 4 ++--
src/nf_modules/sambamba/index_bams.config | 4 ++--
src/nf_modules/sambamba/sort_bams.config | 4 ++--
src/nf_modules/sambamba/split_bams.config | 4 ++--
src/nf_modules/samblaster/dedup_sams.config | 4 ++--
src/nf_modules/samtools/filter_bams.config | 4 ++--
src/nf_modules/samtools/index_bams.config | 4 ++--
src/nf_modules/samtools/sort_bams.config | 4 ++--
src/nf_modules/samtools/split_bams.config | 4 ++--
src/nf_modules/sratoolkit/fastqdump.config | 4 ++--
src/nf_modules/subread/subread.config | 4 ++--
src/nf_modules/urqt/trimming_paired.config | 4 ++--
src/nf_modules/urqt/trimming_single.config | 4 ++--
45 files changed, 93 insertions(+), 88 deletions(-)
create mode 100644 src/conda_psmn.sh
diff --git a/src/conda_psmn.sh b/src/conda_psmn.sh
new file mode 100644
index 00000000..3a91a796
--- /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 aa59cf49..574e6d73 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 91a0fc56..4b554a7b 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 d33ae6c6..49eb9c53 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 d33ae6c6..49eb9c53 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 8c5742cf..5ed9bcc3 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 a5c9b827..bc1c8979 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 a5c9b827..bc1c8979 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 a8e7a27e..4e89c3be 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 b0a49229..aebe28c5 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 2dd2681e..8e62c1cc 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 2dd2681e..8e62c1cc 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 2c8c65a1..f94b4e48 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 2c8c65a1..f94b4e48 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 72056176..13952d87 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 3eb067b5..ea4bab25 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 7068f94c..18483547 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 c2fcafa5..6cece587 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 c2fcafa5..6cece587 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 75d352bc..6731be65 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 75d352bc..6731be65 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 80cf1ea0..01646ee1 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 cc6255c2..8d1d4472 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 d5783a2b..8a038dd9 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 175b0f92..8ac5af00 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 175b0f92..8ac5af00 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 ef11303d..d9a72019 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 295a824d..40754658 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 f4325094..f440d146 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 8d00ba92..d0841719 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 0b40f13b..d49f444a 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 15bdaa8a..90eaae70 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 15bdaa8a..90eaae70 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 7d19d20b..d1dd2c3a 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 c77b4b32..145fa48d 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 b37dade1..afd305f9 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 08a0a633..0b4f093b 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 06a63e48..69f9664f 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 09e97bb4..49bc53f8 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 0cb3bf1f..8436342a 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 34523d0f..eb4468d9 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 9e6bd198..ad33eec9 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 d08b7b85..4e8e0340 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 3f09a7e5..ccc10311 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 0d2254d5..a9806ceb 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
--
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