Merge pull request #34 from icgc-argo/prep-sanger-qc.0.1.3.0

Prep sanger qc.0.1.3.0

tools/prep-sanger-qc/prep-sanger-qc.nf

@@ -23,16 +23,20 @@
  */
 
 nextflow.preview.dsl = 2
-version = '0.1.2.0'
+version = '0.1.3.0'
 
 params.qc_files = ""
+params.publish_dir = ""
+
 params.container_version = ""
 params.cpus = 1
 params.mem = 2  // in GB
 
 
 process prepSangerQc {
   container "quay.io/icgc-argo/prep-sanger-qc:prep-sanger-qc.${params.container_version ?: version}"
+  publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
+
   cpus params.cpus
   memory "${params.mem} GB"
 

tools/prep-sanger-qc/prep-sanger-qc.py

@@ -79,7 +79,7 @@ def get_genotyped_extra_info(file_path):
 
 def main(args):
     description = {
-        'bas': 'Alignment QC metrics generated by Sanger bas_stats.pl script',
+        'bas': 'Alignment QC metrics generated by Sanger bam_stats tool',
         'ascat': 'Purity and ploidy estimated by ASCAT',
         'contamination': 'Cross sample contamination estimated by Sanger verifyBamHomChk.pl script',
         'genotyped': 'Compare genotypes of CRAM files from the same donor and produces the fraction of matched genotypes. It also checks if the inferred genders are matched.'

tools/prep-sanger-qc/tests/checker.nf

@@ -33,7 +33,4 @@ workflow {
     prepSangerQc(
       Channel.fromPath(params.qc_files).collect()
     )
-
-  publish:
-    prepSangerQc.out to: "outdir", overwrite: true
 }