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Verified Commit 565ffad2 authored by Laurent Modolo's avatar Laurent Modolo
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fix ccin2p3 profile for loading miniconda3

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with 21 additions and 21 deletions
src/nf_modules/bedtools/fasta_from_bed.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/bowtie/indexing.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/bowtie/mapping_paired.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/bowtie/mapping_single.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/bowtie2/indexing.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/bowtie2/mapping_paired.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/bowtie2/mapping_single.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/bwa/indexing.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/bwa/mapping_paired.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/cutadapt/adaptor_removal_paired.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/cutadapt/adaptor_removal_single.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/cutadapt/trimming_paired.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/cutadapt/trimming_single.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/deeptools/bam_to_bigwig.config
+ 2
− 2
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/deeptools/compute_matrix.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/deeptools/plot_profile.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/fastp/fastp_paired.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/fastp/fastp_single.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/fastqc/fastqc_paired.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
src/nf_modules/fastqc/fastqc_single.config
+ 1
− 1
View file @ 565ffad2
......@@ -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"
......
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