Merge pull request #1535 from matthdsm/tool/bamtools-split

modules/bamtools/split/main.nf

@@ -2,10 +2,10 @@ process BAMTOOLS_SPLIT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
+    conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
-        'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
+        'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' :
+        'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -20,10 +20,14 @@ process BAMTOOLS_SPLIT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def input_list = bam.collect{"-in $it"}.join(' ')
     """
     bamtools \\
+        merge \\
+        $input_list \\
+        | bamtools \\
             split \\
-        -in $bam \\
+            -stub $prefix \\
             $args
 
     cat <<-END_VERSIONS > versions.yml

modules/bamtools/split/meta.yml

@@ -23,7 +23,7 @@ input:
         e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
-      description: A BAM file to split
+      description: A list of one or more BAM files to merge and then split
       pattern: "*.bam"
 
 output:
@@ -43,3 +43,4 @@ output:
 
 authors:
   - "@sguizard"
+  - "@matthdsm"

tests/modules/bamtools/split/main.nf

@@ -2,13 +2,29 @@
 
 nextflow.enable.dsl = 2
 
-include { BAMTOOLS_SPLIT } from '../../../../modules/bamtools/split/main.nf'
+include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_SINGLE   } from '../../../../modules/bamtools/split/main.nf'
+include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_MULTIPLE } from '../../../../modules/bamtools/split/main.nf'
 
-workflow test_bamtools_split {
+workflow test_bamtools_split_single_input {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
 
-    BAMTOOLS_SPLIT ( input )
+    BAMTOOLS_SPLIT_SINGLE ( input )
 }
+
+workflow test_bamtools_split_multiple {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+        ]
+    ]
+
+    BAMTOOLS_SPLIT_MULTIPLE ( input )
+}
+

tests/modules/bamtools/split/test.yml

@@ -1,10 +1,23 @@
-- name: bamtools split test_bamtools_split
-  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
+- name: bamtools split test_bamtools_split_single_input
+  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_single_input -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
   tags:
-    - bamtools/split
     - bamtools
+    - bamtools/split
   files:
-    - path: output/bamtools/test.paired_end.sorted.REF_chr22.bam
+    - path: output/bamtools/test.REF_chr22.bam
       md5sum: b7dc50e0edf9c6bfc2e3b0e6d074dc07
-    - path: output/bamtools/test.paired_end.sorted.REF_unmapped.bam
+    - path: output/bamtools/test.REF_unmapped.bam
       md5sum: e0754bf72c51543b2d745d96537035fb
+    - path: output/bamtools/versions.yml
+
+- name: bamtools split test_bamtools_split_multiple
+  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_multiple -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/split
+  files:
+    - path: output/bamtools/test.REF_chr22.bam
+      md5sum: 585675bea34c48ebe9db06a561d4b4fa
+    - path: output/bamtools/test.REF_unmapped.bam
+      md5sum: 16ad644c87b9471f3026bc87c98b4963
+    - path: output/bamtools/versions.yml