reformatted input to tuple

software/gatk4/splitncigarreads/main.nf

@@ -20,9 +20,7 @@ process GATK4_SPLITNCIGARREADS {
 
     input:
     tuple val(meta), path(bam)
-    path(fasta)
-    path(fai)
-    path(dict)
+    tuple path(fasta), path(fai), path(dict)
 
     output:
     tuple val(meta), path('*.split_cigar.bam'), emit: bam

software/gatk4/splitncigarreads/meta.yml

@@ -44,9 +44,10 @@ input:
       description: BAM/SAM/CRAM file containing reads
       pattern: "*.{bam,sam,cram}"
   - fasta:
-      type: file
-      description: Reference sequence file
-      pattern: "*.fasta"
+      type: tuple of files
+      description: |
+        Tuple of fasta file (first), sequence dict (second) and fasta index (third)
+      pattern: ["*.fasta", "*.dict", "*.fai"]
 output:
   - bam:
       type: file

tests/software/gatk4/splitncigarreads/main.nf

@@ -10,9 +10,9 @@ workflow test_gatk4_splitncigarreads {
     input = [ [ id:'test' ], // meta map
               [ file("${launchDir}/tests/data/bam/sarscov2_aln.bam", checkIfExists: true)] ]
 
-    fasta = file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
-    fai = file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna.fai", checkIfExists: true)
-    dict = file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.dict", checkIfExists: true)
+    fasta = [ file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true),
+              file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna.fai", checkIfExists: true),
+              file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.dict", checkIfExists: true)]
 
-    GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict )
+    GATK4_SPLITNCIGARREADS ( input, fasta )
 }

tests/software/gatk4/splitncigarreads/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config
   tags:
     - gatk4
-    - gatk4_mergevcfs
+    - gatk4_splitncigarreads
   files:
-    - path: output/gatk4/test.merged.vcf.gz
-      md5sum: f25850b7bd4d362b5ea67d4453e9df55
+    - path: output/gatk4/test.split_cigar.bam
+      md5sum: 9228ac79882a4929c797c891b1bd9f6d