From 4cef5bd781be21ecb80de664d1a8c5eba980f304 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Mon, 19 Feb 2024 09:01:11 +0000
Subject: [PATCH] Tidy up new bits of fastq_align_star (#4939)

* Tidy up new bits of fastq_align_star

* Fix snapshot
---
 subworkflows/nf-core/fastq_align_star/main.nf    |  4 ++--
 .../nf-core/fastq_align_star/tests/main.nf.test  | 16 ++++++++--------
 .../fastq_align_star/tests/main.nf.test.snap     |  4 ++--
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/subworkflows/nf-core/fastq_align_star/main.nf b/subworkflows/nf-core/fastq_align_star/main.nf
index 5208042bce8..980ab8aab36 100644
--- a/subworkflows/nf-core/fastq_align_star/main.nf
+++ b/subworkflows/nf-core/fastq_align_star/main.nf
@@ -13,7 +13,7 @@ workflow FASTQ_ALIGN_STAR {
     val_seq_platform            // string : sequencing platform
     val_seq_center              // string : sequencing center
     ch_fasta                    // channel: [ val(meta), path(fasta) ]
-    ch_transcripts_fasta        // channel: [ path(fasta) ]
+    ch_transcripts_fasta        // channel: [ val(meta), path(fasta) ]
 
     main:
 
@@ -38,7 +38,7 @@ workflow FASTQ_ALIGN_STAR {
     // STAR_ALIGN.out.bam_transcript is populated
     //
 
-    BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME ( STAR_ALIGN.out.bam_transcript, ch_transcripts_fasta.map{[[:], it]} )
+    BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME ( STAR_ALIGN.out.bam_transcript, ch_transcripts_fasta )
 
     emit:
 
diff --git a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test
index e9c6f25ded5..2c512c96518 100644
--- a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test
@@ -28,10 +28,10 @@ nextflow_workflow {
                 """
             }
         }
-    }    
+    }
 
     test("homo_sapiens - fastq - single_end") {
-       config "./nextflow.config"
+        config "./nextflow.config"
         when {
             workflow {
                 """
@@ -51,7 +51,7 @@ nextflow_workflow {
                     [ id:'test_fasta' ], // meta map
                     [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
                 ])
-                input[7] = Channel.of([])
+                input[7] = Channel.of([[:], []])
                 """
             }
         }
@@ -106,7 +106,7 @@ nextflow_workflow {
                     [ id:'test_fasta' ], // meta map
                     [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
                 ])
-                input[7] = Channel.of([])
+                input[7] = Channel.of([[:], []])
                 """
             }
         }
@@ -145,7 +145,7 @@ nextflow_workflow {
                 script "../../../../modules/nf-core/rsem/preparereference/main.nf"
                 process {
                     """
-		    input[0] = channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkifexists: true))
+                    input[0] = channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkifexists: true))
                     input[1] = channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkifexists: true))
                     """
                 }
@@ -173,7 +173,7 @@ nextflow_workflow {
                     [ id:'test_fasta' ], // meta map
                     [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
                 ])
-                input[7] = Channel.of([])
+                input[7] = RSEM_PREPAREREFERENCE.out.transcript_fasta.map{[[:], it]}
                 """
             }
         }
@@ -203,7 +203,7 @@ nextflow_workflow {
             )
         }
     }
-    
+
     test("homo_sapiens - fastq - paired_end - transcripts - no_transcriptome") {
         config "./with_transcripts.config"
 
@@ -229,7 +229,7 @@ nextflow_workflow {
                     [ id:'test_fasta' ], // meta map
                     [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
                 ])
-                input[7] = Channel.of([])
+                input[7] = Channel.of([[:], []])
                 """
             }
         }
diff --git a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap
index be4e7ebcbac..d5fdb713e3a 100644
--- a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap
@@ -463,7 +463,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.sorted.bam.stats:md5,fa2f10820ffe578ebe7d5935155b4366"
+                    "test.sorted.bam.stats:md5,8b4b458a77eb4ffb04a568de36ecb677"
                 ]
             ]
         ],
@@ -471,7 +471,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-16T11:04:06.802475225"
+        "timestamp": "2024-02-16T18:17:49.016776458"
     },
     "orig_bam_transcript_paired_end_transcripts_no_transcriptome": {
         "content": [