update for singularity

nextflow.config

-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'
+}

workflow/main.nf

@@ -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}
   """
 }