diff --git a/tools/prep-sanger-qc/prep-sanger-qc.nf b/tools/prep-sanger-qc/prep-sanger-qc.nf index f8d1352..778bda3 100644 --- a/tools/prep-sanger-qc/prep-sanger-qc.nf +++ b/tools/prep-sanger-qc/prep-sanger-qc.nf @@ -23,9 +23,11 @@ */ 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 @@ -33,6 +35,8 @@ 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" diff --git a/tools/prep-sanger-qc/prep-sanger-qc.py b/tools/prep-sanger-qc/prep-sanger-qc.py index a65e6d9..c3043aa 100755 --- a/tools/prep-sanger-qc/prep-sanger-qc.py +++ b/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.' diff --git a/tools/prep-sanger-qc/tests/checker.nf b/tools/prep-sanger-qc/tests/checker.nf index 4396d43..b6679c6 100755 --- a/tools/prep-sanger-qc/tests/checker.nf +++ b/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 }