From 80360705ca43c369405385f52c34a6de157411fa Mon Sep 17 00:00:00 2001 From: Andrea Haessly Date: Tue, 25 Aug 2020 16:44:04 -0400 Subject: [PATCH 1/2] update awk to split only on tabs to work around sample id with a space --- scripts/mitochondria_m2_wdl/AlignAndCall.wdl | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/scripts/mitochondria_m2_wdl/AlignAndCall.wdl b/scripts/mitochondria_m2_wdl/AlignAndCall.wdl index 4f36f0a370e..4604c156e8e 100644 --- a/scripts/mitochondria_m2_wdl/AlignAndCall.wdl +++ b/scripts/mitochondria_m2_wdl/AlignAndCall.wdl @@ -310,11 +310,11 @@ task GetContamination { fi grep -v "SampleID" output-noquotes > output-data - awk '{print $2}' output-data > contamination.txt - awk '{print $6}' output-data > major_hg.txt - awk '{print $8}' output-data > minor_hg.txt - awk '{print $14}' output-data > mean_het_major.txt - awk '{print $15}' output-data > mean_het_minor.txt + awk -F "\t" '{print $2}' output-data > contamination.txt + awk -F "\t" '{print $6}' output-data > major_hg.txt + awk -F "\t" '{print $8}' output-data > minor_hg.txt + awk -F "\t" '{print $14}' output-data > mean_het_major.txt + awk -F "\t" '{print $15}' output-data > mean_het_minor.txt >>> runtime { preemptible: select_first([preemptible_tries, 5]) From 3345a7bc9869ab16c314a42f0348c218ccfbf400 Mon Sep 17 00:00:00 2001 From: Andrea Haessly Date: Tue, 25 Aug 2020 16:50:39 -0400 Subject: [PATCH 2/2] fix referenced version --- scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl b/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl index cc213df0068..7bbadf67718 100644 --- a/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl +++ b/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl @@ -2,7 +2,7 @@ version 1.0 import "AlignAndCall.wdl" as AlignAndCall -#import "https://api.firecloud.org/ga4gh/v1/tools/mitochondria:AlignAndCall/versions/24/plain-WDL/descriptor" as AlignAndCall +#import "https://api.firecloud.org/ga4gh/v1/tools/mitochondria:AlignAndCall/versions/23/plain-WDL/descriptor" as AlignAndCall workflow MitochondriaPipeline {