Update samtools view (#2098)

* samtools view update

* remove csi output

* prettier

* update meta

* add index functionality

* prettier

* fixed test checks

modules/samtools/view/main.nf

@@ -12,10 +12,13 @@ process SAMTOOLS_VIEW {
     path fasta
 
     output:
-    tuple val(meta), path("*.bam") , emit: bam , optional: true
+    tuple val(meta), path("*.bam"),  emit: bam,     optional: true
-    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    tuple val(meta), path("*.cram"), emit: cram,    optional: true
-    tuple val(meta), path("*.sam") , emit: sam , optional: true
+    tuple val(meta), path("*.sam"),  emit: sam,     optional: true
-    path  "versions.yml"           , emit: versions
+    tuple val(meta), path("*.bai"),  emit: bai,     optional: true
+    tuple val(meta), path("*.csi"),  emit: csi,     optional: true
+    tuple val(meta), path("*.crai"), emit: crai,    optional: true
+    path  "versions.yml",            emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -35,8 +38,8 @@ process SAMTOOLS_VIEW {
         --threads ${task.cpus-1} \\
         ${reference} \\
         $args \\
-        $input \\
+        -o ${prefix}.${file_type} \\
-        > ${prefix}.${file_type}
+        $input
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/samtools/view/meta.yml

@@ -51,6 +51,19 @@ output:
       type: file
       description: optional filtered/converted SAM file
       pattern: "*.{sam}"
+  # bai, csi, and crai are created with `--write-index`
+  - bai:
+      type: file
+      description: optional BAM file index
+      pattern: "*.{bai}"
+  - csi:
+      type: file
+      description: optional tabix BAM file index
+      pattern: "*.{csi}"
+  - crai:
+      type: file
+      description: optional CRAM file index
+      pattern: "*.{crai}"
   - versions:
       type: file
       description: File containing software versions

tests/modules/samtools/view/main.nf

@@ -33,6 +33,16 @@ workflow test_samtools_view_convert {
     SAMTOOLS_VIEW ( input, fasta )
 }
 
+workflow test_samtools_view_index {
+    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)
+
+    SAMTOOLS_VIEW ( input, fasta )
+}
+
 workflow test_samtools_view_stubs {
     input = [ [ id:'test', single_end:false ], // meta map
                 file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),

tests/modules/samtools/view/nextflow.config

@@ -6,4 +6,8 @@ process {
         ext.args = "--output-fmt bam"
     }
 
+    withName: 'test_samtools_view_index:SAMTOOLS_VIEW' {
+        ext.args = "--output-fmt bam --write-index"
+    }
+
 }

tests/modules/samtools/view/test.yml

@@ -5,7 +5,7 @@
     - samtools/view
   files:
     - path: output/samtools/test.bam
-      md5sum: 8fb1e82f76416e9e30fc6b2357e2cf13
+      md5sum: e6a9285be7b1c616dc4e17679fce5f1e
 
 - 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
@@ -14,7 +14,6 @@
     - samtools/view
   files:
     - path: output/samtools/test.cram
-      md5sum: 792399d4d7afc9e58ffeedc1073291b9
 
 - 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
@@ -23,7 +22,18 @@
     - samtools/view
   files:
     - path: output/samtools/test.bam
-      md5sum: 3877632410d032e91a91b054c906a310
+      md5sum: 4f4a97da17db79c78b1912da3cdc1d8f
+
+- 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
+  files:
+    - path: output/samtools/test.bam
+      md5sum: b2d2482cea94adfc9628473792b0d215
+    - path: output/samtools/test.bam.csi
+      md5sum: 343a2085b436cab2123147dafd255607
 
 - 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
@@ -32,4 +42,4 @@
     - samtools/view
   files:
     - path: output/samtools/test.bam
-      md5sum: 8fb1e82f76416e9e30fc6b2357e2cf13
+      md5sum: e6a9285be7b1c616dc4e17679fce5f1e