refactor(prepare_genome): bundle fasta_fai as a tuple emit

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.

Author: pinin4fjords

main.nf

@@ -88,7 +88,7 @@ workflow NFCORE_RNASEQ {
     // SUBWORKFLOW: Build or load aligner / pseudo-aligner / filtering indices
     //
     PREPARE_GENOME_INDICES (
-        PREPARE_GENOME_REFERENCES.out.fasta,
+        PREPARE_GENOME_REFERENCES.out.fasta_fai,
         PREPARE_GENOME_REFERENCES.out.gtf,
         PREPARE_GENOME_REFERENCES.out.transcript_fasta,
         PREPARE_GENOME_REFERENCES.out.rrna_fastas,
@@ -118,8 +118,8 @@ workflow NFCORE_RNASEQ {
     if (!params.skip_alignment && !params.bam_csi_index) {
         PREPARE_GENOME_REFERENCES
             .out
-            .fai
-            .map { fai -> checkMaxContigSize(fai) }
+            .fasta_fai
+            .map { _meta, _fasta, fai -> checkMaxContigSize(fai) }
     }
 
     //
@@ -135,9 +135,8 @@ workflow NFCORE_RNASEQ {
 
     RNASEQ (
         ch_samplesheet,
-        PREPARE_GENOME_REFERENCES.out.fasta,
+        PREPARE_GENOME_REFERENCES.out.fasta_fai,
         PREPARE_GENOME_REFERENCES.out.gtf,
-        PREPARE_GENOME_REFERENCES.out.fai,
         PREPARE_GENOME_REFERENCES.out.chrom_sizes,
         PREPARE_GENOME_REFERENCES.out.gene_bed,
         PREPARE_GENOME_REFERENCES.out.transcript_fasta,

subworkflows/local/prepare_genome_indices/main.nf

@@ -28,7 +28,7 @@ include { STAR_GENOMEPARAMS_UPGRADE         } from '../../../modules/local/star_
 workflow PREPARE_GENOME_INDICES {
 
     take:
-    ch_fasta                 // channel: path(genome.fasta) - emitted from PREPARE_GENOME_REFERENCES
+    ch_fasta_fai             // channel: [ meta, path(genome.fasta), path(genome.fai) ] - emitted from PREPARE_GENOME_REFERENCES
     ch_gtf                   // channel: path(genome.gtf) - emitted from PREPARE_GENOME_REFERENCES
     ch_transcript_fasta      // channel: path(transcript.fasta) - emitted from PREPARE_GENOME_REFERENCES
     ch_rrna_fastas           // channel: path(rrna_fastas) - emitted from PREPARE_GENOME_REFERENCES
@@ -54,6 +54,8 @@ workflow PREPARE_GENOME_INDICES {
     star_index_legacy        // boolean: whether the supplied star_index was built with STAR 2.6.x and needs genomeParameters.txt upgraded to the 2.7.4a metadata schema
 
     main:
+    ch_fasta = ch_fasta_fai.map { _meta, fasta_file, _fai -> fasta_file }
+
     //------------------------------------------------
     // 1) Determine which indices we actually want built
     //------------------------------------------------