From 9a87af7f7245af22e2a06b4029e38f04449debfd Mon Sep 17 00:00:00 2001 From: William Rowell Date: Sat, 10 Aug 2024 10:20:13 -0700 Subject: [PATCH] Minor changes to satisfy linter. --- wdl/tasks/merge_bam_stats.wdl | 2 +- wdl/tasks/pbsv.wdl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/wdl/tasks/merge_bam_stats.wdl b/wdl/tasks/merge_bam_stats.wdl index ec8edb0..2dd3718 100644 --- a/wdl/tasks/merge_bam_stats.wdl +++ b/wdl/tasks/merge_bam_stats.wdl @@ -55,7 +55,7 @@ task merge_bam_stats { Int disk_size = 10 command <<< - zcat ~{sep = " " bam_stats} > ~{sample_id}.read_length_and_quality.tsv + zcat ~{sep=" " bam_stats} > ~{sample_id}.read_length_and_quality.tsv cat << EOF > bin_length.py import sys, pandas as pd diff --git a/wdl/tasks/pbsv.wdl b/wdl/tasks/pbsv.wdl index 0cb8c96..a82a956 100644 --- a/wdl/tasks/pbsv.wdl +++ b/wdl/tasks/pbsv.wdl @@ -149,7 +149,7 @@ task pbsv_call { # This is brittle and likely to break if pbsv discover changes output format. # Build a pattern to match; we want headers (e.g., '^#') and signature # records where third column matches the chromosome (e.g., '^.\t.\tchr1\t'). - pattern=$(echo ~{sep=" " regions} \ + pattern=$(echo ~{sep=" " select_first([regions])} \ | sed 's/^/^.\\t.\\t/; s/ /\\t\|^.\\t.\\t/g; s/$/\\t/' \ | echo "^#|""$(