feat: add minibwa modules (index and map)#12175
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Add an nf-core module wrapping `minibwa index`, which builds an FM-index for a reference genome. minibwa is a reimplementation of bwa-mem for aligning short and accurate long reads. The module emits the index directory of .l2b/.mbw files and a versions topic, and is tested against the sarscov2 genome fasta plus a stub run.
Add an nf-core module wrapping `minibwa map`, which aligns FastQ reads to a minibwa index. The module mirrors bwamem3/mem: it pipes alignments through samtools sort/view (selected by the `sort_bam` input) to emit SAM/BAM/CRAM plus optional indices, and broadcasts the minibwa and samtools versions to the versions topic. Tests cover single- and paired-end sarscov2 reads with sort on/off and a stub run, chaining minibwa/index in setup.
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Description
Adds two new modules for minibwa, a reimplementation of bwa-mem for aligning short and accurate long reads:
minibwa/index— builds the.l2b/.mbwFM-index for a reference genome.minibwa/map— aligns FastQ reads to a minibwa index, piping throughsamtools sort/view(via thesort_baminput) to emit SAM/BAM/CRAM plus optional indices.Both are tested against the sarscov2 genome/fastq fixtures with stub runs.
PR checklist
label.bioconda::minibwa=0.2; Seqera Wave community containers).nf-core modules test minibwa/index --profile dockerandminibwa/mappass.topic: versions.