Update samtools view (#2096)

* samtools view update

* remove csi output

* prettier

* update meta

modules/samtools/view/main.nf

@@ -14,7 +14,7 @@ process SAMTOOLS_VIEW {
     output:
     tuple val(meta), path("*.bam") , emit: bam , optional: true
     tuple val(meta), path("*.cram"), emit: cram, optional: true
-    tuple val(meta), path("*.csi") , emit: csi,  optional: true
+    tuple val(meta), path("*.sam") , emit: sam , optional: true
     path  "versions.yml"           , emit: versions
 
     when:
@@ -22,10 +22,12 @@ process SAMTOOLS_VIEW {
 
     script:
     def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reference = fasta ? "--reference ${fasta} -C" : ""
+    def reference = fasta ? "--reference ${fasta}" : ""
-    def file_type = input.getExtension()
+    def file_type = args.contains("--output-fmt sam") ? "sam" :
+                    args.contains("--output-fmt bam") ? "bam" :
+                    args.contains("--output-fmt cram") ? "cram" :
+                    input.getExtension()
     if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     samtools \\
@@ -34,7 +36,6 @@ process SAMTOOLS_VIEW {
         ${reference} \\
         $args \\
         $input \\
-        $args2 \\
         > ${prefix}.${file_type}
 
     cat <<-END_VERSIONS > versions.yml

modules/samtools/view/meta.yml

@@ -41,21 +41,22 @@ output:
         e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
-      description: filtered/converted BAM/SAM file
+      description: optional filtered/converted BAM file
-      pattern: "*.{bam,sam}"
+      pattern: "*.{bam}"
   - cram:
       type: file
-      description: filtered/converted CRAM file
+      description: optional filtered/converted CRAM file
-      pattern: "*.cram"
+      pattern: "*.{cram}"
+  - sam:
+      type: file
+      description: optional filtered/converted SAM file
+      pattern: "*.{sam}"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - csi:
-      type: file
-      description: BAM index file (optional)
-      pattern: "*.csi"
 authors:
   - "@drpatelh"
   - "@joseespinosa"
   - "@FriederikeHanssen"
+  - "@priyanka-surana"

tests/modules/samtools/view/main.nf

@@ -15,8 +15,18 @@ workflow test_samtools_view {
 
 workflow test_samtools_view_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']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+            ]
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    SAMTOOLS_VIEW ( input, fasta )
+}
+
+workflow test_samtools_view_convert {
+    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)
 

tests/modules/samtools/view/nextflow.config

@@ -2,4 +2,8 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    withName: 'test_samtools_view_convert:SAMTOOLS_VIEW' {
+        ext.args = "--output-fmt bam"
+    }
+
 }

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/view
     - samtools
+    - samtools/view
   files:
     - path: output/samtools/test.bam
       md5sum: 8fb1e82f76416e9e30fc6b2357e2cf13
@@ -10,15 +10,26 @@
 - 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/view
     - samtools
+    - samtools/view
   files:
     - path: output/samtools/test.cram
+      md5sum: 792399d4d7afc9e58ffeedc1073291b9
 
-- name: samtools view test_samtools_view_stubs
+- name: samtools view test_samtools_view_convert
-  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_stubs -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config -stub-run
+  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/view
     - samtools
+    - samtools/view
   files:
     - path: output/samtools/test.bam
+      md5sum: 3877632410d032e91a91b054c906a310
+
+- 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
+  files:
+    - path: output/samtools/test.bam
+      md5sum: 8fb1e82f76416e9e30fc6b2357e2cf13