feat: add fgumi modules and bump fgumi family to 0.4.0#12178
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Add an nf-core module wrapping `fgumi fastq`. Convert a BAM file to interleaved gzipped FASTQ. Mirrors the existing fgumi modules and is pinned to fgumi 0.4.0. Tested against the nf-core UMI test fixtures with a stub run.
Add an nf-core module wrapping `fgumi simplex-metrics`. Collect QC metrics for simplex (single-strand) UMI sequencing data from a UMI-grouped BAM. Mirrors the existing fgumi modules and is pinned to fgumi 0.4.0. Tested against the nf-core UMI test fixtures with a stub run.
Add an nf-core module wrapping `fgumi codec`. Call CODEC consensus reads from a UMI-grouped BAM. Mirrors the existing fgumi modules and is pinned to fgumi 0.4.0. Tested against the nf-core UMI test fixtures with a stub run.
Add an nf-core module wrapping `fgumi downsample`. Downsample a BAM by UMI family using a streaming algorithm. Mirrors the existing fgumi modules and is pinned to fgumi 0.4.0. Tested against the nf-core UMI test fixtures with a stub run.
Add an nf-core module wrapping `fgumi correct`. Correct UMIs in a BAM file (RX tag) to a fixed set of known UMIs (supplied via task.ext.args). Mirrors the existing fgumi modules and is pinned to fgumi 0.4.0. Tested against the nf-core UMI test fixtures with a stub run.
Add an nf-core module wrapping `fgumi clip`. Clip overlapping reads in a queryname-sorted BAM, regenerating tags against a reference FASTA. Mirrors the existing fgumi modules and is pinned to fgumi 0.4.0. Tested against the nf-core UMI test fixtures with a stub run.
Add an nf-core module wrapping `fgumi zipper`. Zip an unmapped UMI BAM together with its aligned BAM, transferring UMI tags onto the aligned reads. Mirrors the existing fgumi modules and is pinned to fgumi 0.4.0. Tested against the nf-core UMI test fixtures with a stub run.
Add an nf-core module wrapping `fgumi dedup`. Mark or remove PCR duplicates using UMI information; emits the deduplicated BAM, metrics, and a family-size histogram. Mirrors the existing fgumi modules and is pinned to fgumi 0.4.0. Tested against the nf-core UMI test fixtures with a stub run.
Bump the eight existing fgumi modules (extract, group, simplex, duplex, duplexmetrics, filter, sort, merge) from fgumi 0.2.0 to 0.4.0 so the entire fgumi module family pins the latest release. Updates the conda pins and both container URLs, and regenerates the nf-test snapshots.
nh13
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Ugh, 8 new modules in one PR :( |
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Description
Adds eight new modules for fgumi, high-performance tools for UMI-tagged sequencing data, and bumps the entire fgumi module family to
fgumi=0.4.0(the latest release):New modules:
fgumi/fastq— convert a BAM to interleaved gzipped FASTQ.fgumi/simplexmetrics— collect QC metrics for simplex UMI data.fgumi/codec— call CODEC consensus reads from a grouped BAM.fgumi/downsample— downsample a BAM by UMI family.fgumi/correct— correct UMIs to a fixed set of known UMIs.fgumi/clip— clip overlapping reads against a reference.fgumi/zipper— zip an unmapped UMI BAM with its aligned BAM.fgumi/dedup— mark/remove PCR duplicates using UMI information.Version bump:
extract,group,simplex,duplex,duplexmetrics,filter,sort,merge) are bumped fromfgumi=0.2.0tofgumi=0.4.0, so all sixteenfgumi/*modules pin the same latest release. Snapshots regenerated accordingly.Each new module is tested against the nf-core UMI test fixtures (with setup chains via
fgumi/extract,fgumi/sort, andsamtools/sortwhere required) plus stub runs.fgumi/reviewis intentionally left for a follow-up PR as it requires a dedicated VCF + consensus/grouped BAM fixture set.PR checklist
fgumi/*modules).label.bioconda::fgumi=0.4.0; Seqera Wave community container).nf-core modules test fgumi/<sub> --profile dockerpasses for all sixteen modules.topic: versions.