small update to samtools/merge (#1896)

modules/samtools/merge/main.nf

@@ -8,8 +8,9 @@ process SAMTOOLS_MERGE {
         'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
-    tuple val(meta), path(input_files)
+    tuple val(meta), path(input_files, stageAs: "?/*")
     path fasta
+    path fai
 
     output:
     tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam

modules/samtools/merge/meta.yml

@@ -29,6 +29,10 @@ input:
       type: optional file
       description: Reference file the CRAM was created with
       pattern: "*.{fasta,fa}"
+  - fai:
+      type: optional file
+      description: Index of the reference file the CRAM was created with
+      pattern: "*.fai"
 output:
   - meta:
       type: map

tests/modules/samtools/merge/main.nf

@@ -6,20 +6,24 @@ include { SAMTOOLS_MERGE } from '../../../../modules/samtools/merge/main.nf'
 
 workflow test_samtools_merge {
     input = [ [ id: 'test' ], // meta map
-               [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                 file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)]
-               ]
+              [ 
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
+              ]
+            ]
 
-    SAMTOOLS_MERGE ( input, [] )
+    SAMTOOLS_MERGE ( input, [], [] )
 }
 
 workflow test_samtools_merge_cram {
     input = [ [ id: 'test' ], // meta map
-               [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-                 file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-                 ]
-               ]
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    SAMTOOLS_MERGE ( input, fasta )
+              [ 
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+              ]
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    SAMTOOLS_MERGE ( input, fasta, fai )
 }

tests/modules/samtools/merge/nextflow.config

@@ -2,8 +2,4 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: SAMTOOLS_MERGE {
-        ext.prefix = { "${meta.id}_merged" }
-    }
-
 }

tests/modules/samtools/merge/test.yml

@@ -4,7 +4,7 @@
     - samtools
     - samtools/merge
   files:
-    - path: output/samtools/test_merged.bam
+    - path: output/samtools/test.bam
 
 - name: samtools merge test_samtools_merge_cram
   command: nextflow run ./tests/modules/samtools/merge -entry test_samtools_merge_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/merge/nextflow.config
@@ -12,4 +12,4 @@
     - samtools
     - samtools/merge
   files:
-    - path: output/samtools/test_merged.cram
+    - path: output/samtools/test.cram