Fix channel issues after updating nf-core/modules

Author: drpatelh

subworkflows/local/align_star/main.nf

@@ -9,8 +9,8 @@ include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools'
 workflow ALIGN_STAR {
     take:
     reads               // channel: [ val(meta), [ reads ] ]
-    index               // channel: /path/to/star/index/
-    gtf                 // channel: /path/to/genome.gtf
+    index               // channel: [ val(meta), [ index ] ]
+    gtf                 // channel: [ val(meta), [ gtf ] ]
     star_ignore_sjdbgtf // boolean: when using pre-built STAR indices do not re-extract and use splice junctions from the GTF file 
     seq_platform        // string : sequencing platform
     seq_center          // string : sequencing center

subworkflows/local/prepare_genome/main.nf

@@ -191,7 +191,7 @@ workflow PREPARE_GENOME {
                 ch_star_index = STAR_GENOMEGENERATE_IGENOMES ( ch_fasta, ch_gtf ).index
                 ch_versions   = ch_versions.mix(STAR_GENOMEGENERATE_IGENOMES.out.versions)
             } else {
-                ch_star_index = STAR_GENOMEGENERATE ( ch_fasta, ch_gtf ).index
+                ch_star_index = STAR_GENOMEGENERATE ( ch_fasta.map { [ [:], it ] }, ch_gtf.map { [ [:], it ] } ).index.map { it[1] }
                 ch_versions   = ch_versions.mix(STAR_GENOMEGENERATE.out.versions)
             }
         }

workflows/rnaseq.nf

@@ -382,8 +382,8 @@ workflow RNASEQ {
     if (!params.skip_alignment && params.aligner == 'star_salmon') {
         ALIGN_STAR (
             ch_filtered_reads,
-            PREPARE_GENOME.out.star_index,
-            PREPARE_GENOME.out.gtf,
+            PREPARE_GENOME.out.star_index.map { [ [:], it ] },
+            PREPARE_GENOME.out.gtf.map { [ [:], it ] },
             params.star_ignore_sjdbgtf,
             '',
             params.seq_center ?: '',
@@ -729,7 +729,7 @@ workflow RNASEQ {
         if (!params.skip_qualimap) {
             QUALIMAP_RNASEQ (
                 ch_genome_bam,
-                PREPARE_GENOME.out.gtf
+                PREPARE_GENOME.out.gtf.map { [ [:], it ] }
             )
             ch_qualimap_multiqc = QUALIMAP_RNASEQ.out.results
             ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions.first())