From c604c42bb92a6301b13a250582eabed509adaae1 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Mon, 25 Oct 2021 20:02:45 +0000 Subject: [PATCH] Bugfix .bai secondary file for ApplyBSQR behavior no issue # Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl | 2 +- .../cwl/helper/gatk-haplotypecaller-with-interval.cwl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl index 52413a6..f6d625a 100644 --- a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl @@ -54,7 +54,7 @@ outputs: format: edam:format_2572 # BAM label: Recalibrated BAM for given interval secondaryFiles: - - .bai + - ^.bai outputBinding: glob: "*nodups_BQSR.bam" diff --git a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl index 4b3d1a7..0b6c102 100644 --- a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl @@ -25,7 +25,7 @@ inputs: format: edam:format_2572 # BAM label: Recalibrated BAM for given interval secondaryFiles: - - .bai + - ^.bai reference: type: File format: edam:format_1929 # FASTA -- 2.30.2