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Fix/reorganize results #75

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merged 2 commits into from
Jan 3, 2024
Merged

Fix/reorganize results #75

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645b7f3
fix stub
MarieLataretu Jan 3, 2024
bfdc856
publish (un)mapped_merged with keep
MarieLataretu Jan 3, 2024
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4 changes: 3 additions & 1 deletion modules/alignment_processing.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ process filter_true_dcs_alignments {
"""
stub:
"""
touch ${name}.no-dcs.bam ${name}.true-dcs.bam ${name}.false-dcs.bam ${name}.no-dcs.bam.bai ${name}.true-dcs.bam.bai ${name}.false-dcs.bam.bai
touch ${name}.no-dcs.bam ${name}.true-dcs.bam ${name}.false-dcs.bam ${name}.no-dcs.bam.bai ${name}.true-dcs.bam.bai ${name}.false-dcs.bam.bai dcs.bam dcs.bam.bai
"""
}

Expand Down Expand Up @@ -154,6 +154,8 @@ process fastq_from_bam {
fn.matches('.*.soft-clipped_merged.fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.soft-clipped_merged(.fast[aq].gz)$', '$1') :
fn.matches('.*.unmapped_(1|2|singleton).fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.unmapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') :
fn.matches('.*.mapped_(1|2|singleton).fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.mapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') :
fn.matches('.*.unmapped_merged_(1|2|singleton).fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.unmapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') :
fn.matches('.*.mapped_merged_(1|2|singleton).fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.mapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') :
fn
}
)
Expand Down
2 changes: 2 additions & 0 deletions modules/utils.nf
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Expand Up @@ -108,6 +108,8 @@ process filter_fastq_by_name {
fn.matches('.*.fast[aq].contamination.fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.fast[aq].contamination(.fast[aq].gz)$', '$1') :
fn.matches('.*.unmapped_(1|2|singleton).fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.unmapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') :
fn.matches('.*.mapped_(1|2|singleton).fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.mapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') :
fn.matches('.*.unmapped_merged_(1|2|singleton).fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.unmapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') :
fn.matches('.*.mapped_merged_(1|2|singleton).fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.mapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') :
fn
}
)
Expand Down