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docs(modkit/pileup): clarify BAM index, BED format, and --cpg requirements #10341

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docs(modkit/pileup): clarify BAM index, BED format, and --cpg requirements #10341

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docs(modkit/pileup): clarify BAM index, BED format, and --cpg require…
sahuno Mar 6, 2026
950e6c6
docs(modkit/pileup): use modkit's exact BED errors, document --includ…
sahuno Sep 6, 2026
665761d
Merge branch 'master' into fix/modkit-pileup-meta-docs
sahuno Sep 11, 2026
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16 changes: 12 additions & 4 deletions modules/nf-core/modkit/pileup/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,9 @@ input:
ontologies: []
- bai:
type: file
description: Associated index file for BAM
pattern: "*.bai"
description: Associated index file for BAM. Both BAI and CSI indices
are supported by modkit (via htslib).
pattern: "*.{bai,csi}"
ontologies: []
- - meta2:
type: map
Expand All @@ -37,7 +38,9 @@ input:
- fasta:
type: file
description: Reference sequence in FASTA format. Required for motif (e.g.
CpG) filtering
CpG) filtering. Note that when using --cpg via ext.args, you must also
pass --modified-bases (e.g. '--cpg --modified-bases 5mC') or modkit
will error with a missing required argument.
pattern: "*.fasta"
ontologies: []
- fai:
Expand All @@ -53,7 +56,12 @@ input:
- bed:
type: file
description: BED file that will restrict threshold estimation and pileup
results to positions overlapping intervals in the file
results to positions overlapping intervals in the file. Must be in
BED3 (chr, start, end) or BED6 format; modkit rejects other column
counts with "improperly formatted BED line, must be BED3 or BED6"
followed by "zero valid positions parsed from BED file". Note also
that modkit requires --motif or --modified-bases in ext.args whenever
--include-bed is used, and errors out otherwise.
pattern: "*.bed"
ontologies: []
output:
Expand Down