From e52b3887b70aab1881b1c821f09040548b469590 Mon Sep 17 00:00:00 2001 From: Roman Valls Guimera Date: Mon, 7 May 2018 10:02:46 +1000 Subject: [PATCH] grch37 assembly by default, grch38 still has some bugs that need to be resolved first: https://github.com/sigven/pcgr/issues/27 --- ansible/files/pcgr_consumer.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/ansible/files/pcgr_consumer.py b/ansible/files/pcgr_consumer.py index 9fb3325..ee5cbd7 100644 --- a/ansible/files/pcgr_consumer.py +++ b/ansible/files/pcgr_consumer.py @@ -57,13 +57,14 @@ def process(sample): cleanup(sample) os.mkdir(output_dir) - cmdline = "/mnt/pcgr/pcgr.py --force_overwrite --input_vcf {vcf}.vcf.gz {somatic_flags} /mnt/pcgr {output} {conf}.toml {sample}" + cmdline = "/mnt/pcgr/pcgr.py --force_overwrite --input_vcf {vcf}.vcf.gz {somatic_flags} /mnt/pcgr {output} {genome_assembly} {conf}.toml {sample}" if sample.endswith("-somatic"): cmdline = cmdline.format(vcf=sample, conf=sample, output=output_dir, sample=sample, + genome_assembly="grch37", somatic_flags="--input_cna {}.tsv".format(sample)) log.info("Processing somatic sample {sample} with commandline {cli}".format(sample=sample, cli=cmdline)) @@ -73,6 +74,7 @@ def process(sample): conf=sample, output=output_dir, sample=sample, + genome_assembly="grch37", somatic_flags='') log.info("Processing normal sample {sample} with commandline: {cli}".format(sample=sample, cli=cmdline))