Add subsample and branch hic_mapping #192
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Isn't hic_bamtobed only filtering, not subsampling as thats the prior step? |
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I was just trying to indicate that this use of bam to bed, incorporated the subsampling step, to distinguish from the version used for cooler. I will reword to clarify. |
DLBPointon
reviewed
Jan 11, 2024
subworkflows/local/hic_mapping.nf
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| @@ -210,32 +210,37 @@ workflow HIC_MAPPING { | |||
| // ch_versions = ch_versions.mix ( SNAPSHOT_HRES.out.versions ) | |||
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| // | |||
| // MODULE: MERGE POSITION SORTED BAM FILES AND MARK DUPLICATES | |||
| // MODULE: SUBSAMPLE BAM IF OVER 50G | |||
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Would it be better to check file size and use an if block if size over 50G prior to the module. This would then stop a container being spun up just to mv a file (in the case file < 50G). Then the module can focus on subsampling.
Something akin to:
file = input.map{ it -> it[1] }
if ( file.size() > 50G ) {
SUB_SAMPLE(input)
fixed_ch = SUB_SAMPLE.out.subsampled
} else {
fixed_ch = input
}
yumisims
reviewed
Jan 11, 2024
modules/local/subsample_bam.nf
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| percentage=`wc -c !{mergedbam} | cut -d$' ' -f1 | awk '{printf "%.2f\\n", 50000000000 / $0}'` | ||
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| if awk "BEGIN {exit !($percentage <= 1 )}"; then | ||
| samtools view -s $percentage -b !{mergedbam} > !{meta.id}_subsampled.bam |
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which to change? The one in the if is being removed. The samtools parameter is referencing a shell variable, whilst {mergedbam} is a nextflow.
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).Closes Hi-C Mapping - Subset for juicer hi-c #158