add extra output from snap aligner (#1826)

modules/snapaligner/align/main.nf

@@ -13,6 +13,7 @@ process SNAPALIGNER_ALIGN {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.bai"), optional: true, emit: bai
     path "versions.yml"           , emit: versions
 
     when:

modules/snapaligner/align/meta.yml

@@ -43,6 +43,9 @@ output:
       type: file
       description: Aligned BAM file
       pattern: "*.{bam}"
-
+  - bai:
+      type: file
+      description: Optional aligned BAM file index
+      pattern: "*.{bai}"
 authors:
   - "@matthdsm"

tests/modules/snapaligner/align/main.nf

@@ -2,9 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { SNAPALIGNER_INDEX                       } from '../../../../modules/snapaligner/index/main.nf'
-include { SNAPALIGNER_ALIGN as SNAPALIGNER_SINGLE } from '../../../../modules/snapaligner/align/main.nf'
-include { SNAPALIGNER_ALIGN as SNAPALIGNER_PAIRED } from '../../../../modules/snapaligner/align/main.nf'
+include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
+include { SNAPALIGNER_ALIGN } from '../../../../modules/snapaligner/align/main.nf'
 
 workflow test_snapaligner_single {
 
@@ -14,7 +13,7 @@ workflow test_snapaligner_single {
     ]
 
     SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
-    SNAPALIGNER_SINGLE ( input, SNAPALIGNER_INDEX.out.index )
+    SNAPALIGNER_ALIGN ( input, SNAPALIGNER_INDEX.out.index )
 }
 
 workflow test_snapaligner_paired {
@@ -25,5 +24,5 @@ workflow test_snapaligner_paired {
     ]
 
     SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
-    SNAPALIGNER_PAIRED ( input, SNAPALIGNER_INDEX.out.index )
+    SNAPALIGNER_ALIGN ( input, SNAPALIGNER_INDEX.out.index )
 }

tests/modules/snapaligner/align/nextflow.config

@@ -1,5 +1,9 @@
 process {
-
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
+    withName: SNAPALIGNER_INDEX {
+        publishDir = [ enabled: false ]
+    }
+    withName: SNAPALIGNER_ALIGN {
+        ext.args = "-so"
+    }
+}

tests/modules/snapaligner/align/test.yml

@@ -1,19 +1,21 @@
 - name: snapaligner align test_snapaligner_single
-  command: nextflow run tests/modules/snapaligner/align -entry test_snapaligner_single -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/snapaligner/align -entry test_snapaligner_single -c ./tests/config/nextflow.config  -c ./tests/modules/snapaligner/align/nextflow.config
   tags:
     - snapaligner/align
     - snapaligner
   files:
     - path: output/snapaligner/test.bam
-      md5sum: 5d95594e4ef1ee23ce56e6a7cb64f0f2
-    - path: output/snapaligner/versions.yml
+      md5sum: 2dea536f28c041c1108add3523879243
+    - path: output/snapaligner/test.bam.bai
+      md5sum: 3f5cd1e8379b06554778a59b179ccc10
 
 - name: snapaligner align test_snapaligner_paired
-  command: nextflow run tests/modules/snapaligner/align -entry test_snapaligner_paired -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/snapaligner/align -entry test_snapaligner_paired -c ./tests/config/nextflow.config  -c ./tests/modules/snapaligner/align/nextflow.config
   tags:
     - snapaligner/align
     - snapaligner
   files:
     - path: output/snapaligner/test.bam
-      md5sum: a1405da5876f15dbe8a81516b94c2a15
-    - path: output/snapaligner/versions.yml
+      md5sum: 941bf870355dd34ebe2ef43ea41abcc4
+    - path: output/snapaligner/test.bam.bai
+      md5sum: ce7fd5bc6f0196e6ad70d3710e17e559