Commit 5288e775 authored by Brandi Cantarel's avatar Brandi Cantarel

update for singularity

parent 2d53d37c
Pipeline #8089 failed with stage
in 2 seconds
process.executor='slurm'
process.queue='128GB,256GB,256GBv1'
process.clusterOptions = '--hold'
trace.enabled = false
trace.file = 'pipeline_trace.txt'
trace.field = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime'
params {
repoDir='/seqprg'
}
process {
executor = 'slurm'
clusterOptions = '--hold --no-kill'
queue = '128GB,256GB,256GBv1'
withLabel: trim {
container = 'goalconsortium/trim_galore:1.0.4'
}
withLabel: dnaalign {
container = 'goalconsortium/dna_alignment:1.0.4'
}
withLabel: profiling_qc {
container = 'goalconsortium/profiling_qc:1.0.4'
}
withName: starfusion {
container = 'goalconsortium/starfusion:1.0.4'
}
withName: ralign {
container = 'goalconsortium/rna_alignment:1.0.4'
}
withName: geneabund {
container = 'goalconsortium/rna_gene_abundance:1.0.4'
}
}
singularity {
enabled = true
runOptions='--no-home --cleanenv'
cacheDir = '/project/shared/bicf_workflow_ref/seqprg/singularity/'
}
trace {
enabled = true
file = 'pipeline_trace.txt'
field = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime'
}
timeline {
enabled = false
file = 'timeline.html'
}
report {
enabled = false
file = 'report.html'
}
env {
http_proxy = 'http://proxy.swmed.edu:3128'
https_proxy = 'http://proxy.swmed.edu:3128'
all_proxy = 'http://proxy.swmed.edu:3128'
}
manifest {
homePage = 'https://git.biohpc.swmed.edu/ngsclialab/school'
description = 'School is a collection of genomics analysis workflows that are used for detecting single nucleotide variants (SNVs), insertions/deletions (indels), copy number variants (CNVs) and translocations from RNA and DNA sequencing. These workflows have been validated in a CLIA laboratory at UTSW'
mainScript = 'rna.nf'
version = '1.0.0'
nextflowVersion = '>=0.31.0'
}
......@@ -23,6 +23,11 @@ indel="$params.genome/GoldIndels.vcf.gz"
knownindel=file(indel)
dbsnp=file(dbsnp)
repoDir=workflow.projectDir
if (params.repoDir) {
repoDir=params.repoDir
}
// params genome is the directory
// base name for the index is always genome
index_path = file(params.genome)
......@@ -75,18 +80,20 @@ if( ! read ) { error "Didn't match any input files with entries in the design fi
// Trim raw reads using trimgalore
process trim {
errorStrategy 'ignore'
label 'trim'
input:
set pair_id, file(fqs) from read
output:
set pair_id, file("${pair_id}.trim.R*.fastq.gz") into trimread
script:
"""
bash $baseDir/process_scripts/preproc_fastq/trimgalore.sh -f -p ${pair_id} ${fqs}
bash $repoDir/process_scripts/preproc_fastq/trimgalore.sh -f -p ${pair_id} ${fqs}
"""
}
process align {
process ralign {
errorStrategy 'ignore'
label 'ralign'
publishDir "$params.output", mode: 'copy'
input:
set pair_id, file(fqs) from trimread
......@@ -96,12 +103,13 @@ process align {
file("${pair_id}.alignerout.txt") into hsatout
script:
"""
bash $baseDir/process_scripts/alignment/rnaseqalign.sh -a $params.align -p ${pair_id} -r ${index_path} ${fqs}
bash $repoDir/process_scripts/alignment/rnaseqalign.sh -a $params.align -p ${pair_id} -r ${index_path} ${fqs}
"""
}
process alignqc {
errorStrategy 'ignore'
label 'profiling_qc'
publishDir "$params.output", mode: 'copy'
input:
set pair_id, file(bam) from aligned2
......@@ -110,13 +118,14 @@ process alignqc {
set file("${pair_id}_fastqc.zip"),file("${pair_id}_fastqc.html") into fastqc
script:
"""
bash $baseDir/process_scripts/alignment/bamqc.sh -p ${pair_id} -b ${bam} -y rna
bash $repoDir/process_scripts/alignment/bamqc.sh -p ${pair_id} -b ${bam} -y rna
"""
}
// Identify duplicate reads with Picard
process markdups {
publishDir "$params.output", mode: 'copy'
label 'dnaalign'
input:
set pair_id, file(sbam) from aligned
output:
......@@ -124,7 +133,7 @@ process markdups {
set pair_id, file("${pair_id}.dedup.bam") into deduped2
script:
"""
bash $baseDir/process_scripts/alignment/markdups.sh -a $params.markdups -b $sbam -p $pair_id
bash $repoDir/process_scripts/alignment/markdups.sh -a $params.markdups -b $sbam -p $pair_id
"""
}
......@@ -132,6 +141,7 @@ process markdups {
// Assemble transcripts with stringtie
process geneabund {
errorStrategy 'ignore'
label 'geneabund'
publishDir "$params.output", mode: 'copy'
input:
set pair_id, file(sbam) from deduped1
......@@ -142,7 +152,7 @@ process geneabund {
file("${pair_id}.fpkm.txt") into fpkm
script:
"""
bash $baseDir/process_scripts/genect_rnaseq/geneabundance.sh -s $params.stranded -g ${gtf_file} -p ${pair_id} -b ${sbam}
bash $repoDir/process_scripts/genect_rnaseq/geneabundance.sh -s $params.stranded -g ${gtf_file} -p ${pair_id} -b ${sbam}
"""
}
......
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