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Minor changes to satisfy linter.
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williamrowell committed Aug 10, 2024
1 parent 1ff53b9 commit 9a87af7
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2 changes: 1 addition & 1 deletion wdl/tasks/merge_bam_stats.wdl
Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion wdl/tasks/pbsv.wdl
Original file line number Diff line number Diff line change
Expand Up @@ -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/$/\\t/' \
| echo "^#|""$(</dev/stdin)")
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