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feat: update samtools.smk and remove design_bed as a default extra #112

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merged 4 commits into from
Dec 5, 2023
Merged

feat: update samtools.smk and remove design_bed as a default extra #112

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3627a93
feat: update samtools.smk and remove design_bed as a default extra
padraicc Nov 27, 2023
1e9bee9
Update workflow/rules/samtools.smk
padraicc Dec 5, 2023
df58728
feat: add schemas for samtools rules
padraicc Dec 5, 2023
1e91fee
Update rules.schema.yaml
padraicc Dec 5, 2023
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8 changes: 2 additions & 6 deletions workflow/rules/samtools.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,7 @@ rule samtools_stats:
output:
temp("qc/samtools_stats/{sample}_{type}.samtools-stats.txt"),
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params:
extra="%s -t %s"
% (
config.get("samtools_stats", {}).get("extra", ""),
config.get("reference", {}).get("design_bed", ""),
),
extra=config.get("samtools_stats", {}).get("extra", ""),
log:
"qc/samtools_stats/{sample}_{type}.samtools-stats.txt.log",
benchmark:
Expand All @@ -34,7 +30,7 @@ rule samtools_stats:
message:
"{rule}: calculate qc using samtools for {input.bam}"
wrapper:
"0.79.0/bio/samtools/stats"
"v3.0.0/bio/samtools/stats"


rule samtools_idxstats:
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