Skip to content
Snippets Groups Projects
Unverified Commit e58b21b6 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

nf: change psmn config to use conda

parent 93255688
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 40 additions and 40 deletions
src/nf_modules/fastqc/fastqc_single.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/hisat2/indexing.config
+ 2
− 2
View file @ e58b21b6
......@@ -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"
......
src/nf_modules/htseq/htseq.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/kallisto/indexing.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/kallisto/mapping_paired.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/kallisto/mapping_single.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/macs2/peak_calling.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/multiqc/multiqc_paired.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/multiqc/multiqc_single.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/music/peak_calling_single.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/rsem/indexing.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/rsem/quantification_paired.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/rsem/quantification_single.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/sambamba/index_bams.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/sambamba/sort_bams.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/sambamba/split_bams.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/samblaster/dedup_sams.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/samtools/filter_bams.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/samtools/index_bams.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
src/nf_modules/samtools/sort_bams.config
+ 2
− 2
View file @ e58b21b6
......@@ -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
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment