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Unverified Commit b43a5a48 authored by Laurent Modolo's avatar Laurent Modolo
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conda_psmn: fix path of the scripts in configs files

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src/nf_modules/bedtools/fasta_from_bed.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fasta_from_bed {
beforeScript = "./src/conda_psmn.sh"
conda = "bedtools_2.25.0"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/${CONDA_ENVS}bedtools_2.25.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/bowtie/indexing.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_fasta {
beforeScript = "./src/conda_psmn.sh"
conda = "bowtie_1.2.2"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie_1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
......
src/nf_modules/bowtie/mapping_paired.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
beforeScript = "./src/conda_psmn.sh"
conda = "bowtie/1.2.2:samtools_1.7"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie/1.2.2:samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
......
src/nf_modules/bowtie/mapping_single.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
beforeScript = "./src/conda_psmn.sh"
conda = "bowtie/1.2.2:samtools_1.7"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie/1.2.2:samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
......
src/nf_modules/bowtie2/indexing.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_fasta {
beforeScript = "./src/conda_psmn.sh"
conda = "bowtie2_2.3.4.1"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
......
src/nf_modules/bowtie2/mapping_paired.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
beforeScript = "./src/conda_psmn.sh"
conda = "bowtie2_2.3.4.1"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
......
src/nf_modules/bowtie2/mapping_single.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
beforeScript = "./src/conda_psmn.sh"
conda = "bowtie2_2.3.4.1"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
......
src/nf_modules/bwa/indexing.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_fasta {
beforeScript = "./src/conda_psmn.sh"
conda = "bwa_0.7.17"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bwa_0.7.17"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
......
src/nf_modules/bwa/mapping_paired.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
beforeScript = "./src/conda_psmn.sh"
conda = "bwa_0.7.17"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bwa_0.7.17"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
......
src/nf_modules/cutadapt/adaptor_removal_paired.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: adaptor_removal {
beforeScript = "./src/conda_psmn.sh"
conda = "cutadapt_2.1"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/cutadapt/adaptor_removal_single.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: adaptor_removal {
beforeScript = "./src/conda_psmn.sh"
conda = "cutadapt_2.1"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/cutadapt/trimming_paired.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: trimming {
beforeScript = "./src/conda_psmn.sh"
conda = "cutadapt_2.1"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/cutadapt/trimming_single.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: trimming {
beforeScript = "./src/conda_psmn.sh"
conda = "cutadapt_2.1"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/deeptools/bam_to_bigwig.config
+ 2
− 2
View file @ b43a5a48
......@@ -30,8 +30,8 @@ profiles {
psmn{
process{
withName: index_bam {
beforeScript = "./src/conda_psmn.sh"
conda = "sambamba_0.6.7"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/sambamba_0.6.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
......
src/nf_modules/deeptools/compute_matrix.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: compute_matrix {
beforeScript = "./src/conda_psmn.sh"
conda = "deeptools_3.0.2"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/deeptools_3.0.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
......
src/nf_modules/deeptools/plot_profile.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: plot_profile {
beforeScript = "./src/conda_psmn.sh"
conda = "deeptools_3.0.2"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/deeptools_3.0.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
......
src/nf_modules/fastp/fastp_paired.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastp_fastq {
beforeScript = "./src/conda_psmn.sh"
conda = "fastp_0.19.7"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/fastp_0.19.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/fastp/fastp_single.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastp_fastq {
beforeScript = "./src/conda_psmn.sh"
conda = "fastp_0.19.7"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/fastp_0.19.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/fastqc/fastqc_paired.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastqc_fastq {
beforeScript = "./src/conda_psmn.sh"
conda = "fastqc_0.11.5"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/fastqc_0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
src/nf_modules/fastqc/fastqc_single.config
+ 2
− 2
View file @ b43a5a48
......@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastqc_fastq {
beforeScript = "./src/conda_psmn.sh"
conda = "fastqc_0.11.5"
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/fastqc_0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......
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