feat: add methylsieve module#12182
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LGTM, just these minor comments to be addressed. Thanks for your contribution :)
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Add an nf-core module wrapping `methylsieve`, a fast filter for unconverted reads in methylation (bisulfite/EM-seq) sequencing. It tags (or filters) reads by per-template cytosine conversion against a reference and emits the BAM plus a per-context conversion-rate stats TSV. Runs inline in the alignment pipe (aligner -> methylsieve -> sort). Tested against the sarscov2 paired-end alignment fixture + reference with a stub run.
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Description
Adds a module for methylsieve, a fast, robust filter for unconverted reads in methylation sequencing (bisulfite / EM-seq). For each template it tallies monitored cytosines against the reference and tags (or filters) incompletely-converted reads, emitting the BAM plus a per-context / per-spike-in conversion-rate statistics TSV. It runs inline in the alignment pipe (
aligner | methylsieve | samtools sort).Tested against the sarscov2 paired-end alignment fixture + reference (with
.fai) and a stub run.PR checklist
label.bioconda::methylsieve=0.1.0; Seqera Wave community container).nf-core modules test methylsieve --profile dockerpasses.topic: versions.