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fix: indexed bam files can now be put as input #1378

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merged 2 commits into from May 25, 2023
Merged

fix: indexed bam files can now be put as input #1378

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8e3b286
fix: indexed bam files can now be put as input
jonca79 May 25, 2023
9b38127
test: added bai file to test example
jonca79 May 25, 2023
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1 change: 1 addition & 0 deletions bio/gatk/variantannotator/test/Snakefile
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Expand Up @@ -2,6 +2,7 @@ rule gatk_annotator:
input:
vcf="calls/snvs.vcf.gz",
aln="mapped/a.bam",
bai="mapped/a.bam.bai",
ref="genome.fasta",
db="calls/snvs.vcf.gz",
# intervals="targets.bed",
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2 changes: 1 addition & 1 deletion bio/gatk/variantannotator/wrapper.py
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Expand Up @@ -32,7 +32,7 @@
resources = [
f"--resource:{name} {file}"
for name, file in snakemake.input.items()
if name not in ["vcf", "aln", "ref", "known", "intervals"]
if name not in ["vcf", "aln", "ref", "known", "intervals", "bai"]
]


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