Merge pull request #1851 from nf-core/refactor/split-prepare-genome

Split PREPARE_GENOME into REFERENCES + INDICES subworkflows

Author: pinin4fjords

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1848](https://github.com/nf-core/rnaseq/pull/1848) - Align `actions/checkout` SHA in `nf-test-arm.yml` and `nf-test-gpu.yml` with the template-derived `nf-test.yml` (`v6`) ([#1847](https://github.com/nf-core/rnaseq/issues/1847))
 - [PR #1849](https://github.com/nf-core/rnaseq/pull/1849) - Tidy-up batch addressing [#1845](https://github.com/nf-core/rnaseq/issues/1845): README/schema clarifications, `&` → `&&` in three guards, deduplicated `withName` blocks, and removal of the unmaintained `bin/fastq_dir_to_samplesheet.py` (use [nf-core/fetchngs](https://nf-co.re/fetchngs) for samplesheet generation)
 - [PR #1850](https://github.com/nf-core/rnaseq/pull/1850) - Use the active aligner's display name in the MultiQC `fail_mapped` per-sample status row, and drop the hardcoded "STAR" reference from the pipeline-completion `min_mapped_reads` warning, so Bowtie2 reports no longer mislabel the metric as STAR ([#1846](https://github.com/nf-core/rnaseq/issues/1846))
+- [PR #1851](https://github.com/nf-core/rnaseq/pull/1851) - Split `PREPARE_GENOME` into `PREPARE_GENOME_REFERENCES` (FASTA / GTF / BED / transcript FASTA / chrom.sizes / rRNA / Kraken DB) and `PREPARE_GENOME_INDICES` (per-aligner index build/load) for clearer ownership; no user-facing parameter, output, or behaviour change ([#1721](https://github.com/nf-core/rnaseq/issues/1721)).
 - [PR #1852](https://github.com/nf-core/rnaseq/pull/1852) - Flatten `workflows/rnaseq/assets/` back to top-level `assets/` so `nf-core pipelines bump-version` finds `assets/multiqc_config.yml` and updates the report-comment URLs automatically on release bumps
 
 ## [[3.26.0](https://github.com/nf-core/rnaseq/releases/tag/3.26.0)] - 2026-05-07

conf/modules/prepare_genome.config

@@ -78,7 +78,7 @@ process {
         ]
     }
 
-    withName: '.*:PREPARE_GENOME:BOWTIE2_BUILD' {
+    withName: '.*:PREPARE_GENOME_INDICES:BOWTIE2_BUILD' {
         publishDir = [
             path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
             mode: params.publish_dir_mode,
@@ -165,7 +165,7 @@ process {
         ]
     }
 
-    withName: '.*:PREPARE_GENOME:BBMAP_BBSPLIT' {
+    withName: '.*:PREPARE_GENOME_INDICES:BBMAP_BBSPLIT' {
         ext.args   = 'build=1'
         ext.prefix = 'genome_transcriptome'
         publishDir = [

main.nf

@@ -36,13 +36,14 @@ params.bowtie2_index    = getGenomeAttribute('bowtie2')
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { RNASEQ                  } from './workflows/rnaseq'
-include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
-include { checkMaxContigSize      } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
-include { defineQcTools           } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
-include { isStarIndexLegacy       } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
+include { RNASEQ                     } from './workflows/rnaseq'
+include { PREPARE_GENOME_REFERENCES  } from './subworkflows/local/prepare_genome_references'
+include { PREPARE_GENOME_INDICES     } from './subworkflows/local/prepare_genome_indices'
+include { PIPELINE_INITIALISATION    } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
+include { PIPELINE_COMPLETION        } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
+include { checkMaxContigSize         } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
+include { defineQcTools              } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
+include { isStarIndexLegacy          } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -58,18 +59,42 @@ workflow NFCORE_RNASEQ {
     main:
 
     //
-    // SUBWORKFLOW: Prepare reference genome files
+    // SUBWORKFLOW: Prepare reference genome files (FASTA, GTF, BED, transcript FASTA, chrom.sizes, rRNA FASTAs, Kraken DB)
     //
-    PREPARE_GENOME (
+    PREPARE_GENOME_REFERENCES (
         params.fasta,
         params.gtf,
         params.gff,
         params.additional_fasta,
         params.transcript_fasta,
         params.gene_bed,
+        params.ribo_database_manifest,
+        params.kraken_db,
+        params.gencode,
+        params.gffread_transcript_fasta,
+        params.featurecounts_group_type,
+        params.aligner,
+        params.pseudo_aligner,
+        params.skip_gtf_filter,
+        params.remove_ribo_rna ? params.ribo_removal_tool : null,
+        params.skip_alignment,
+        params.skip_pseudo_alignment,
+        params.use_sentieon_star,
+        params.contaminant_screening,
+        params.prokaryotic ?: false
+    )
+
+    //
+    // SUBWORKFLOW: Build or load aligner / pseudo-aligner / filtering indices
+    //
+    PREPARE_GENOME_INDICES (
+        PREPARE_GENOME_REFERENCES.out.fasta_fai,
+        PREPARE_GENOME_REFERENCES.out.gtf,
+        PREPARE_GENOME_REFERENCES.out.transcript_fasta,
+        PREPARE_GENOME_REFERENCES.out.rrna_fastas,
+        params.fasta ? true : false,
         params.splicesites,
         params.bbsplit_fasta_list,
-        params.ribo_database_manifest,
         params.star_index,
         params.rsem_index,
         params.salmon_index,
@@ -78,30 +103,23 @@ workflow NFCORE_RNASEQ {
         params.bowtie2_index,
         params.bbsplit_index,
         params.sortmerna_index,
-        params.kraken_db,
-        params.gencode,
-        params.gffread_transcript_fasta,
-        params.featurecounts_group_type,
         params.aligner,
         params.pseudo_aligner,
-        params.skip_gtf_filter,
         params.skip_bbsplit,
         params.remove_ribo_rna ? params.ribo_removal_tool : null,
         params.skip_alignment,
         params.skip_pseudo_alignment,
         params.use_sentieon_star,
         params.use_parabricks_star,
-        params.contaminant_screening,
-        params.prokaryotic ?: false,
         isStarIndexLegacy() ?: false
     )
 
     // Check if contigs in genome fasta file > 512 Mbp
     if (!params.skip_alignment && !params.bam_csi_index) {
-        PREPARE_GENOME
+        PREPARE_GENOME_REFERENCES
             .out
-            .fai
-            .map { fai -> checkMaxContigSize(fai) }
+            .fasta_fai
+            .map { _meta, _fasta, fai -> checkMaxContigSize(fai) }
     }
 
     //
@@ -110,31 +128,30 @@ workflow NFCORE_RNASEQ {
     ch_samplesheet = channel.value(file(params.input, checkIfExists: true))
 
     // Bowtie2 rRNA index is built on-demand inside the fastq_remove_rrna subworkflow
-    // rather than in PREPARE_GENOME, to avoid duplicating the rRNA FASTA preparation logic
+    // rather than in PREPARE_GENOME_INDICES, to avoid duplicating the rRNA FASTA preparation logic
     ch_bowtie2_rrna_index = channel.empty()
 
     def qc_tools = defineQcTools(params)
 
     RNASEQ (
         ch_samplesheet,
-        PREPARE_GENOME.out.fasta,
-        PREPARE_GENOME.out.gtf,
-        PREPARE_GENOME.out.fai,
-        PREPARE_GENOME.out.chrom_sizes,
-        PREPARE_GENOME.out.gene_bed,
-        PREPARE_GENOME.out.transcript_fasta,
-        PREPARE_GENOME.out.star_index,
-        PREPARE_GENOME.out.rsem_index,
-        PREPARE_GENOME.out.hisat2_index,
-        PREPARE_GENOME.out.bowtie2_index,
-        PREPARE_GENOME.out.salmon_index,
-        PREPARE_GENOME.out.kallisto_index,
-        PREPARE_GENOME.out.bbsplit_index,
-        PREPARE_GENOME.out.rrna_fastas,
-        PREPARE_GENOME.out.sortmerna_index,
+        PREPARE_GENOME_REFERENCES.out.fasta_fai,
+        PREPARE_GENOME_REFERENCES.out.gtf,
+        PREPARE_GENOME_REFERENCES.out.chrom_sizes,
+        PREPARE_GENOME_REFERENCES.out.gene_bed,
+        PREPARE_GENOME_REFERENCES.out.transcript_fasta,
+        PREPARE_GENOME_INDICES.out.star_index,
+        PREPARE_GENOME_INDICES.out.rsem_index,
+        PREPARE_GENOME_INDICES.out.hisat2_index,
+        PREPARE_GENOME_INDICES.out.bowtie2_index,
+        PREPARE_GENOME_INDICES.out.salmon_index,
+        PREPARE_GENOME_INDICES.out.kallisto_index,
+        PREPARE_GENOME_INDICES.out.bbsplit_index,
+        PREPARE_GENOME_REFERENCES.out.rrna_fastas,
+        PREPARE_GENOME_INDICES.out.sortmerna_index,
         ch_bowtie2_rrna_index,
-        PREPARE_GENOME.out.splicesites,
-        PREPARE_GENOME.out.kraken_db,
+        PREPARE_GENOME_INDICES.out.splicesites,
+        PREPARE_GENOME_REFERENCES.out.kraken_db,
         qc_tools
     )
 

nf-test.config

@@ -14,7 +14,7 @@ config {
 
     def baseIgnore = ['modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*']
     def sentieonTests = ['tests/sentieon_default.nf.test', 'subworkflows/local/align_star/tests/main.sentieon.nf.test']
-    def gpuTests = ['tests/parabricks_default.nf.test', 'tests/gpu_ribodetector.nf.test', 'subworkflows/local/align_star/tests/main.parabricks.nf.test', 'subworkflows/local/prepare_genome/tests/main.parabricks.nf.test']
+    def gpuTests = ['tests/parabricks_default.nf.test', 'tests/gpu_ribodetector.nf.test', 'subworkflows/local/align_star/tests/main.parabricks.nf.test', 'subworkflows/local/prepare_genome_indices/tests/main.parabricks.nf.test']
 
     ignore = baseIgnore + (skipSentieon ? sentieonTests : []) + (skipGpu ? gpuTests : [])