Split PREPARE_GENOME into REFERENCES + INDICES subworkflows#1851
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Closes #1721. PREPARE_GENOME's 33-input take block split into two focused subworkflows: PREPARE_GENOME_REFERENCES (FASTA/GTF/BED/transcript fasta/chrom.sizes/rRNA/Kraken DB) and PREPARE_GENOME_INDICES (per-aligner index build/load). No user-facing parameter, output, or behaviour change. [skip ci]
…-genome # Conflicts: # CHANGELOG.md
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Overall good - I'm adding a comment on whether this is the best strategy or should we organise it differently but that's up for debate.
Per review feedback (#1851 r3209803147), emit fasta+fai as [meta, fasta, fai] from PREPARE_GENOME_REFERENCES. INDICES, main.nf, and the RNASEQ workflow take block updated to consume the tuple directly; the previous ad-hoc combine in workflows/rnaseq/main.nf that rebuilt this triple is dropped. Snapshots regenerated.
…aseq into refactor/split-prepare-genome
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Summary
Closes #1721.
Splits the 33-input
PREPARE_GENOMEsubworkflow into two focused subworkflows:PREPARE_GENOME_REFERENCES(~20 inputs): FASTA / GTF / BED / transcript FASTA / chrom.sizes / rRNA FASTAs / Kraken DBPREPARE_GENOME_INDICES(~24 inputs): per-aligner index build/load (STAR, RSEM, HISAT2, Bowtie2, Salmon, Kallisto, BBSplit, SortMeRNA)Logic moved verbatim, only restructured. No user-facing parameter, output, or behaviour change.
main.nfnow invokes both in sequence and feeds reference channels from_REFERENCESinto_INDICES. DownstreamRNASEQworkflow'stakeblock is unchanged.The 43 + 2 existing tests are split across the two new subworkflow test directories. Snapshot assertions for bare-path channels were rewritten as
[file(p).name, path(p).md5]closures to work around an nf-test 0.9.5 / Nextflow 25.04.3 issue where bare-path serialization is non-deterministic when many tests share an invocation.Test plan
nf-testfor both new subworkflows🤖 Generated with Claude Code