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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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10 changes: 3 additions & 7 deletions workflow/rules/samtools.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -8,13 +8,9 @@ rule samtools_stats:
input:
bam="alignment/samtools_merge_bam/{sample}_{type}.bam",
output:
temp("qc/samtools_stats/{sample}_{type}.samtools-stats.txt"),
stats=temp("qc/samtools_stats/{sample}_{type}.samtools-stats.txt"),
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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41 changes: 41 additions & 0 deletions workflow/schemas/rules.schema.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -405,6 +405,47 @@ properties:
type: string
description: WGS statistics used by MultiQC

samtools_idxstats:
type: object
description: input and output parameters for samtools_idxstats
properties:
input:
type: object
description: list of inputs
properties:
bam:
type: string
description: Aligned bam file
bai:
type: string
description: Bam index file
output:
type: object
description: list of outputs
properties:
stats:
type: string
description: Alignment summary statistics from samtools idxstats

samtools_stats:
type: object
description: input and output parameters for samtools_stats
properties:
input:
type: object
description: list of inputs
properties:
bam:
type: string
description: Aligned bam file
output:
type: object
description: list of outputs
properties:
stats:
type: string
description: Alignment summary statistics from samtools stats

verifybamid2:
type: object
description: input and output parameters for verifybamid2
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