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capturing sambamba/markdup log for MultiQC report #1064

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capturing sambamba/markdup log for MultiQC report #1064

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13a888e
capturing sambamba/markdup log for MultiQC report
Sep 26, 2024
fedc174
missing commas error
Sep 30, 2024
f1964af
Merge branch 'develop' into fix_sambamba_report
katsikora Apr 14, 2025
3d5ca21
Update sambamba.snakefile
katsikora Apr 14, 2025
98a6230
Merge branch 'develop' into fix_sambamba_report
katsikora Apr 14, 2025
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12 changes: 7 additions & 5 deletions snakePipes/shared/rules/sambamba.snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -7,16 +7,18 @@ rule sambamba_markdup:
input:
aligner+"/{sample}.sorted.bam"
output:
aligner+"/{sample}.markdup.bam"# duplicate marked
bam=aligner+"/{sample}.markdup.bam"
log: "Sambamba/{sample}.markdup.txt"
threads: lambda wildcards: 10 if 10<max_thread else max_thread
benchmark: aligner + "/.benchmark/sambamba_markdup.{sample}.benchmark"
params:
tempDir = tempDir
tempDir = tempDir,
buffer = "--sort-buffer-size=6000 --overflow-list-size 600000"
conda: CONDA_SAMBAMBA_ENV
shell: """
TMPDIR={params.tempDir}
MYTEMP=$(mktemp -d "${{TMPDIR:-/tmp}}"/snakepipes.XXXXXXXXXX)
sambamba markdup -t {threads} --sort-buffer-size=6000 --overflow-list-size 600000 --tmpdir $MYTEMP {input} {output}
sambamba markdup -t {threads} {params.buffer} --tmpdir $MYTEMP {input} {output.bam} > {log}
rm -rf "$MYTEMP"
"""

Expand All @@ -25,7 +27,7 @@ rule sambamba_flagstat_sorted:
input:
aligner+"/{sample}.sorted.bam"
output:
"Sambamba/{sample}.sorted.markdup.txt"
"Sambamba/{sample}.sorted.flagstat.txt"
conda: CONDA_SAMBAMBA_ENV
threads: lambda wildcards: 10 if 10<max_thread else max_thread
shell: """
Expand All @@ -36,7 +38,7 @@ rule sambamba_flagstat:
input:
aligner+"/{sample}.markdup.bam"
output:
"Sambamba/{sample}.markdup.txt"
"Sambamba/{sample}.flagstat.txt"
conda: CONDA_SAMBAMBA_ENV
threads: lambda wildcards: 10 if 10<max_thread else max_thread
shell: """
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