Add CRAM to samtools/index (#1049)

* feat: update samtools/index

* feat: add test

* fix: lint

* fix: output file + md5

modules/samtools/index/main.nf

@@ -19,16 +19,17 @@ process SAMTOOLS_INDEX {
     }
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(input)
 
     output:
-    tuple val(meta), path("*.bai"), optional:true, emit: bai
-    tuple val(meta), path("*.csi"), optional:true, emit: csi
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path("*.bai") , optional:true, emit: bai
+    tuple val(meta), path("*.crai"), optional:true, emit: crai
+    tuple val(meta), path("*.csi") , optional:true, emit: csi
+    path  "versions.yml"           , emit: versions
 
     script:
     """
-    samtools index $options.args $bam
+    samtools index $options.args $input
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')

modules/samtools/index/meta.yml

@@ -35,6 +35,10 @@ output:
         type: file
         description: BAM/CRAM/SAM index file
         pattern: "*.{bai,crai,sai}"
+    - crai:
+        type: file
+        description: BAM/CRAM/SAM index file
+        pattern: "*.{bai,crai,sai}"
     - csi:
         type: file
         description: CSI index file
@@ -46,3 +50,4 @@ output:
 authors:
     - "@drpatelh"
     - "@ewels"
+    - "@maxulysse"

tests/modules/samtools/index/main.nf

@@ -2,8 +2,9 @@
 
 nextflow.enable.dsl = 2
 
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI } from '../../../../modules/samtools/index/main.nf' addParams( options: [:] )
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI } from '../../../../modules/samtools/index/main.nf' addParams( options: [args:'-c'] )
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI  } from '../../../../modules/samtools/index/main.nf' addParams( options: [:] )
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CRAI } from '../../../../modules/samtools/index/main.nf' addParams( options: [:] )
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI  } from '../../../../modules/samtools/index/main.nf' addParams( options: [args:'-c'] )
 
 workflow test_samtools_index_bai {
     input = [ [ id:'test', single_end:false ], // meta map
@@ -13,6 +14,14 @@ workflow test_samtools_index_bai {
     SAMTOOLS_INDEX_BAI ( input )
 }
 
+workflow test_samtools_index_crai {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
+            ]
+
+    SAMTOOLS_INDEX_CRAI ( input )
+}
+
 workflow test_samtools_index_csi {
     input = [ [ id:'test', single_end:false ], // meta map
                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)

tests/modules/samtools/index/test.yml

@@ -7,6 +7,15 @@
     - path: output/samtools/test.paired_end.sorted.bam.bai
       md5sum: 704c10dd1326482448ca3073fdebc2f4
 
+- name: samtools index crai
+  command: nextflow run tests/modules/samtools/index -entry test_samtools_index_crai -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/index
+  files:
+    - path: output/samtools/test.paired_end.recalibrated.sorted.cram.crai
+      md5sum: 537e3d8c937bcc4e34e1cf47cd71d484
+
 - name: samtools index csi
   command: nextflow run tests/modules/samtools/index -entry test_samtools_index_csi -c tests/config/nextflow.config
   tags: