add qname feature to samtools/view (#2115)

* add qname feature to samtools_view

* update tests

* Update modules/samtools/view/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/samtools/view/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* added filter tests

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/samtools/view/main.nf

@@ -10,6 +10,7 @@ process SAMTOOLS_VIEW {
     input:
     tuple val(meta), path(input), path(index)
     path fasta
+    path qname
 
     output:
     tuple val(meta), path("*.bam"),  emit: bam,     optional: true
@@ -27,6 +28,7 @@ process SAMTOOLS_VIEW {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--reference ${fasta}" : ""
+    def readnames = qname ? "--qname-file ${qname}": ""
     def file_type = args.contains("--output-fmt sam") ? "sam" :
                     args.contains("--output-fmt bam") ? "bam" :
                     args.contains("--output-fmt cram") ? "cram" :
@@ -37,6 +39,7 @@ process SAMTOOLS_VIEW {
         view \\
         --threads ${task.cpus-1} \\
         ${reference} \\
+        ${readnames} \\
         $args \\
         -o ${prefix}.${file_type} \\
         $input

modules/samtools/view/meta.yml

@@ -33,6 +33,10 @@ input:
       type: optional file
       description: Reference file the CRAM was created with
       pattern: "*.{fasta,fa}"
+  - qname:
+      type: file
+      description: Optional file with read names to output only select alignments
+      pattern: "*.{txt,list}"
 output:
   - meta:
       type: map

tests/modules/samtools/view/main.nf

@@ -10,7 +10,7 @@ workflow test_samtools_view {
                 []
             ]
 
-    SAMTOOLS_VIEW ( input, [] )
+    SAMTOOLS_VIEW ( input, [], [] )
 }
 
 workflow test_samtools_view_cram {
@@ -20,7 +20,7 @@ workflow test_samtools_view_cram {
             ]
     fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
 
-    SAMTOOLS_VIEW ( input, fasta )
+    SAMTOOLS_VIEW ( input, fasta, [] )
 }
 
 workflow test_samtools_view_convert {
@@ -30,7 +30,7 @@ workflow test_samtools_view_convert {
             ]
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
 
-    SAMTOOLS_VIEW ( input, fasta )
+    SAMTOOLS_VIEW ( input, fasta, [] )
 }
 
 workflow test_samtools_view_index {
@@ -40,7 +40,19 @@ workflow test_samtools_view_index {
             ]
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
 
-    SAMTOOLS_VIEW ( input, fasta )
+    SAMTOOLS_VIEW ( input, fasta, [] )
+}
+
+workflow test_samtools_view_filter {
+    input = [ [ id: 'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                []
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    qname = Channel.of("testN:2817", "testN:2814").collectFile(name: "readnames.list", newLine: true)
+
+    SAMTOOLS_VIEW ( input, fasta, qname )
 }
 
 workflow test_samtools_view_stubs {
@@ -49,5 +61,5 @@ workflow test_samtools_view_stubs {
                 []
             ]
 
-    SAMTOOLS_VIEW ( input, [] )
+    SAMTOOLS_VIEW ( input, [], [] )
 }

tests/modules/samtools/view/nextflow.config

@@ -10,4 +10,9 @@ process {
         ext.args = "--output-fmt bam --write-index"
     }
 
+    withName: 'test_samtools_view_filter:SAMTOOLS_VIEW' {
+        ext.args = "--output-fmt bam --write-index"
+    }
+
+
 }

tests/modules/samtools/view/test.yml

@@ -1,8 +1,8 @@
 - name: samtools view test_samtools_view
   command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
   tags:
-    - samtools
     - samtools/view
+    - samtools
   files:
     - path: output/samtools/test.bam
       md5sum: e6a9285be7b1c616dc4e17679fce5f1e
@@ -10,16 +10,16 @@
 - name: samtools view test_samtools_view_cram
   command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_cram -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
   tags:
-    - samtools
     - samtools/view
+    - samtools
   files:
     - path: output/samtools/test.cram
 
 - name: samtools view test_samtools_view_convert
   command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_convert -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
   tags:
-    - samtools
     - samtools/view
+    - samtools
   files:
     - path: output/samtools/test.bam
       md5sum: 4f4a97da17db79c78b1912da3cdc1d8f
@@ -27,19 +27,30 @@
 - name: samtools view test_samtools_view_index
   command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_index -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
   tags:
-    - samtools
     - samtools/view
+    - samtools
   files:
     - path: output/samtools/test.bam
       md5sum: b2d2482cea94adfc9628473792b0d215
     - path: output/samtools/test.bam.csi
       md5sum: 343a2085b436cab2123147dafd255607
 
+- name: samtools view test_samtools_view_filter
+  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_filter -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
+  tags:
+    - samtools/view
+    - samtools
+  files:
+    - path: output/samtools/test.bam
+      md5sum: d8e20876423cb1123a559e4347115249
+    - path: output/samtools/test.bam.csi
+      md5sum: b1d688576e59529271333aa50b3ad3ae
+
 - name: samtools view test_samtools_view_stubs
   command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_stubs -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
   tags:
-    - samtools
     - samtools/view
+    - samtools
   files:
     - path: output/samtools/test.bam
       md5sum: e6a9285be7b1c616dc4e17679fce5f1e