From 565ffad2275bc6ab4b841dbcb5f8f1acf6d71fbf Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 15 May 2019 10:51:49 +0200
Subject: [PATCH] fix ccin2p3 profile for loading miniconda3
---
src/nf_modules/bedtools/fasta_from_bed.config | 2 +-
src/nf_modules/bowtie/indexing.config | 2 +-
src/nf_modules/bowtie/mapping_paired.config | 2 +-
src/nf_modules/bowtie/mapping_single.config | 2 +-
src/nf_modules/bowtie2/indexing.config | 2 +-
src/nf_modules/bowtie2/mapping_paired.config | 2 +-
src/nf_modules/bowtie2/mapping_single.config | 2 +-
src/nf_modules/bwa/indexing.config | 2 +-
src/nf_modules/bwa/mapping_paired.config | 2 +-
src/nf_modules/cutadapt/adaptor_removal_paired.config | 2 +-
src/nf_modules/cutadapt/adaptor_removal_single.config | 2 +-
src/nf_modules/cutadapt/trimming_paired.config | 2 +-
src/nf_modules/cutadapt/trimming_single.config | 2 +-
src/nf_modules/deeptools/bam_to_bigwig.config | 4 ++--
src/nf_modules/deeptools/compute_matrix.config | 2 +-
src/nf_modules/deeptools/plot_profile.config | 2 +-
src/nf_modules/fastp/fastp_paired.config | 2 +-
src/nf_modules/fastp/fastp_single.config | 2 +-
src/nf_modules/fastqc/fastqc_paired.config | 2 +-
src/nf_modules/fastqc/fastqc_single.config | 2 +-
src/nf_modules/hisat2/indexing.config | 2 +-
src/nf_modules/hisat2/mapping_paired.config | 2 +-
src/nf_modules/hisat2/mapping_single.config | 2 +-
src/nf_modules/htseq/htseq.config | 4 ++--
src/nf_modules/kallisto/indexing.config | 2 +-
src/nf_modules/kallisto/mapping_paired.config | 2 +-
src/nf_modules/kallisto/mapping_single.config | 2 +-
src/nf_modules/macs2/peak_calling.config | 2 +-
src/nf_modules/multiqc/multiqc_paired.config | 4 ++--
src/nf_modules/multiqc/multiqc_single.config | 4 ++--
src/nf_modules/music/peak_calling_single.config | 6 +++---
src/nf_modules/rsem/indexing.config | 2 +-
src/nf_modules/rsem/quantification_paired.config | 2 +-
src/nf_modules/rsem/quantification_single.config | 2 +-
src/nf_modules/sambamba/index_bams.config | 2 +-
src/nf_modules/sambamba/sort_bams.config | 2 +-
src/nf_modules/sambamba/split_bams.config | 2 +-
src/nf_modules/samblaster/dedup_sams.config | 2 +-
src/nf_modules/samtools/filter_bams.config | 2 +-
src/nf_modules/samtools/index_bams.config | 2 +-
src/nf_modules/samtools/sort_bams.config | 2 +-
src/nf_modules/samtools/split_bams.config | 2 +-
src/nf_modules/sratoolkit/fastqdump.config | 2 +-
src/nf_modules/urqt/trimming_paired.config | 2 +-
src/nf_modules/urqt/trimming_single.config | 2 +-
45 files changed, 51 insertions(+), 51 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 17dee4b1..7a2e982b 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: fasta_from_bed {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bedtools_2.25.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 627cc943..0f6fd494 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 598b99a1..3582d00f 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 598b99a1..3582d00f 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 966b7a9f..85480186 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 5c975a8c..3584a222 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 5c975a8c..3584a222 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index eeb59fad..4fcea110 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 7b964120..d1f05908 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 6fb8ea64..b635d8a8 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: adaptor_removal {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 6fb8ea64..b635d8a8 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: adaptor_removal {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 0aef1942..3ebf0514 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 0aef1942..3ebf0514 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 30b3b0f9..bf1ebd09 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -55,7 +55,7 @@ profiles {
ccin2p3 {
process{
withName: index_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
scratch = true
stageInMode = "copy"
@@ -69,7 +69,7 @@ profiles {
}
process{
withName: bam_to_bigwig {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index bb3d987f..76ccaa7a 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: compute_matrix {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index de2276e8..eca7b8bb 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: plot_profile {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index b93eccd1..f4b0d892 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: fastp_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index b93eccd1..f4b0d892 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: fastp_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index a74fb951..bdeaeac7 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index a74fb951..bdeaeac7 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index c56f1819..6214ad49 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 23a4acc5..95108b57 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index 23a4acc5..95108b57 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index ec072e0b..90905699 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -49,7 +49,7 @@ profiles {
ccin2p3 {
process{
withName: sort_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
@@ -61,7 +61,7 @@ profiles {
queue = 'huge'
}
withName: counting {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/htseq_0.11.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 501daa09..a89cc5a3 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index bfbbb6b2..f033f789 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index bfbbb6b2..f033f789 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 3538315e..1670ee68 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/macs2_2.1.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 51afdbb3..71fb79fc 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -58,7 +58,7 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
@@ -70,7 +70,7 @@ profiles {
queue = 'huge'
}
withName: multiqc {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index bde67e34..fdc12e4e 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -57,7 +57,7 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
@@ -69,7 +69,7 @@ profiles {
queue = 'huge'
}
withName: multiqc {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index bd7036b0..1dc69007 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -106,7 +106,7 @@ profiles {
}
process{
withName: compute_mappability {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
stageInMode = "copy"
@@ -118,7 +118,7 @@ profiles {
queue = 'huge'
}
withName: music_preprocessing {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
stageInMode = "copy"
@@ -130,7 +130,7 @@ profiles {
queue = 'huge'
}
withName: music_computation {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index 03ee920b..5747a30f 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 4f859c2e..0c1768cc 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 4f859c2e..0c1768cc 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index e8ab95ac..818acc4b 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index a408436b..c4f8ed2d 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: sort_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 4bc3cda1..1a7f7bbb 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: split_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 951d6f87..5f00a51e 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: dedup_sam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samblaster_0.1.24"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index f2f899b6..65d6c697 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: filter_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index d5336bb0..f47469c1 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: index_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 8d1153d2..fd8a8655 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: sort_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 72501731..00a83948 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: split_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 664482e0..a0347be8 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: fastq_dump {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sratoolkit_2.8.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 1b250b39..deedb874 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/urqt_d62c1f8"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index b107cf22..7f7fdc56 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/urqt_d62c1f8"
scratch = true
stageInMode = "copy"
--
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