Skip to content
Snippets Groups Projects
Unverified Commit cbe80128 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

nf_modules: rm ccin2p3_conda section in config files

parent 9ec1ade8
No related branches found
No related tags found
No related merge requests found
Showing
with 0 additions and 380 deletions
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: index_fasta {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: mapping_fastq {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: mapping_fastq {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -51,34 +51,6 @@ profiles { ...@@ -51,34 +51,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: sort_bam {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
withName: counting {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/htseq_0.11.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: index_fasta {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: mapping_fastq {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: mapping_fastq {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: mapping_fastq {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/macs2_2.1.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -56,34 +56,6 @@ profiles { ...@@ -56,34 +56,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: fastqc_fastq {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
withName: multiqc {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -55,34 +55,6 @@ profiles { ...@@ -55,34 +55,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: fastqc_fastq {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
withName: multiqc {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -69,46 +69,6 @@ profiles { ...@@ -69,46 +69,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: compute_mappability {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
withName: music_preprocessing {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
withName: music_computation{
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: index_fasta {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: mapping_fastq {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: mapping_fastq {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: index_bam {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: sort_bam {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: split_bam {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: dedup_sam {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samblaster_0.1.24"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -34,22 +34,6 @@ profiles { ...@@ -34,22 +34,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: filter_bam {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
...@@ -33,22 +33,6 @@ profiles { ...@@ -33,22 +33,6 @@ profiles {
} }
} }
} }
ccin2p3_conda {
process{
withName: index_bam {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 { ccin2p3 {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/" singularity.cacheDir = "/sps/lbmc/common/singularity/"
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment