Commit 9131c8e0 authored by Brandi Cantarel's avatar Brandi Cantarel

update with singularity

parent 5288e775
Pipeline #8178 failed with stage
in 2 seconds
...@@ -6,22 +6,25 @@ process { ...@@ -6,22 +6,25 @@ process {
clusterOptions = '--hold --no-kill' clusterOptions = '--hold --no-kill'
queue = '128GB,256GB,256GBv1' queue = '128GB,256GB,256GBv1'
withLabel: trim { withLabel: trim {
container = 'goalconsortium/trim_galore:1.0.4' container = 'trim_galore.sif'
} }
withLabel: dnaalign { withLabel: dnaalign {
container = 'goalconsortium/dna_alignment:1.0.4' container = 'dna_alignment.sif'
} }
withLabel: profiling_qc { withLabel: profiling_qc {
container = 'goalconsortium/profiling_qc:1.0.4' container = 'profiling_qc.sif'
} }
withName: starfusion { withLabel: starfusion {
container = 'goalconsortium/starfusion:1.0.4' container = 'starfusion.sif'
} }
withName: ralign { withLabel: ralign {
container = 'goalconsortium/rna_alignment:1.0.4' container = 'rna_alignment.sif'
} }
withName: geneabund { withLabel: geneabund {
container = 'goalconsortium/rna_gene_abundance:1.0.4' container = 'rna_gene_abundance.sif'
}
withLabel: rnaseqstat {
container = 'rnaseq_dea.sif'
} }
} }
......
...@@ -34,23 +34,18 @@ index_path = file(params.genome) ...@@ -34,23 +34,18 @@ index_path = file(params.genome)
process checkdesignfile { process checkdesignfile {
queue 'super' queue 'super'
module 'parallel/20150122:pigz/2.4' label 'trim'
publishDir "$params.output", mode: 'copy' publishDir "$params.output", mode: 'copy'
input: input:
file design_file name 'design.ori.txt' file design_file name 'design.ori.txt'
file ("*") from fqs.collect() file ("*") from fqs.collect()
output: output:
file("design.valid.txt") into newdesign file("design.valid.txt") into newdesign
file("*.fastq.gz") into fastqs mode flatten file("*.fastq.gz") into fastqs mode flatten
stdout spltnames stdout spltnames
script: script:
""" """
bash $baseDir/scripts/check_inputfiles.sh bash $repoDir/process_scripts/design_file/checkdesignfile.sh ${params.pairs} design.ori.txt
perl -p -e 's/\\r\\n*/\\n/g' design.ori.txt > design.fix.txt
perl $baseDir/scripts/check_designfile.pl ${params.pairs} design.fix.txt
""" """
} }
...@@ -159,6 +154,7 @@ process geneabund { ...@@ -159,6 +154,7 @@ process geneabund {
process statanal { process statanal {
errorStrategy 'ignore' errorStrategy 'ignore'
publishDir "$params.output", mode: 'copy' publishDir "$params.output", mode: 'copy'
label 'rnaseqstat'
input: input:
file count_file from counts.toList() file count_file from counts.toList()
file count_sum from ctsum.toList() file count_sum from ctsum.toList()
......
Subproject commit 96bcf78802267e8bb1834c06ffb98c5d700273e3 Subproject commit 8706de703b8b5933f89651e5be0312af96cddb7c
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