Add tbi index as an output to lofreq callparallel (nf-core#6427)

Add tbi as an output to lofreq callparallel Co-authored-by: fmartinez <[email protected]>
famosab · Aug 28, 2024 · 9889e36 · 9889e36
1 parent 5a38b71
commit 9889e36
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Showing 4 changed files with 46 additions and 12 deletions.
diff --git a/modules/nf-core/lofreq/callparallel/main.nf b/modules/nf-core/lofreq/callparallel/main.nf
@@ -13,8 +13,9 @@ process LOFREQ_CALLPARALLEL {
     tuple val(meta3), path(fai)
 
     output:
-    tuple val(meta), path("*.vcf.gz"), emit: vcf
-    path "versions.yml"              , emit: versions
+    tuple val(meta), path("*.vcf.gz")    , emit: vcf
+    tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi
+    path "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,8 +34,8 @@ process LOFREQ_CALLPARALLEL {
     samtools_cram_convert += alignment_cram ? "    samtools index ${alignment_out}\n" : ''
 
     def samtools_cram_remove = ''
-    samtools_cram_remove += alignment_cram ? "     rm ${alignment_out}\n" : ''
-    samtools_cram_remove += alignment_cram ? "     rm ${alignment_out}.bai\n " : ''
+    samtools_cram_remove += alignment_cram ? "    rm ${alignment_out}\n" : ''
+    samtools_cram_remove += alignment_cram ? "    rm ${alignment_out}.bai\n " : ''
     """
     $samtools_cram_convert
 
@@ -59,6 +60,7 @@ process LOFREQ_CALLPARALLEL {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo "" | gzip > ${prefix}.vcf.gz
+    echo "" | gzip > ${prefix}.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/lofreq/callparallel/meta.yml b/modules/nf-core/lofreq/callparallel/meta.yml
@@ -62,6 +62,10 @@ output:
       type: file
       description: Predicted variants file
       pattern: "*.{vcf}"
+  - tbi:
+      type: file
+      description: Index of vcf file
+      pattern: "*.{vcf.gz.tbi}"
 authors:
   - "@kaurravneet4123"
   - "@bjohnnyd"

diff --git a/modules/nf-core/lofreq/callparallel/tests/main.nf.test b/modules/nf-core/lofreq/callparallel/tests/main.nf.test
@@ -32,7 +32,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match() },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.tbi.collect { file(it[1]).getName() }
+                    ).match() },
                 { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains('##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">') }
             )
         }
@@ -62,7 +65,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match() },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.tbi.collect { file(it[1]).getName() }
+                    ).match() },
                 { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains('##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">') }
             )
         }

diff --git a/modules/nf-core/lofreq/callparallel/tests/main.nf.test.snap b/modules/nf-core/lofreq/callparallel/tests/main.nf.test.snap
@@ -11,8 +11,24 @@
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,1a60c330fb42841e8dcf3cd507a70bfc"
+                    ]
+                ],
+                "2": [
                     "versions.yml:md5,56d45e0015add277b2689f071a4fe3e4"
                 ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,1a60c330fb42841e8dcf3cd507a70bfc"
+                    ]
+                ],
                 "vcf": [
                     [
                         {
@@ -28,32 +44,38 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nextflow": "23.04.0"
         },
-        "timestamp": "2024-07-10T12:57:00.731035"
+        "timestamp": "2024-08-28T12:01:24.268196316"
     },
     "sarscov2 - bam": {
         "content": [
             [
                 "versions.yml:md5,56d45e0015add277b2689f071a4fe3e4"
+            ],
+            [
+                "test.vcf.gz.tbi"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nextflow": "23.04.0"
         },
-        "timestamp": "2024-07-10T12:59:23.105421"
+        "timestamp": "2024-08-28T12:28:18.229899904"
     },
     "sarscov2 - bam - bed": {
         "content": [
             [
                 "versions.yml:md5,56d45e0015add277b2689f071a4fe3e4"
+            ],
+            [
+                "test.vcf.gz.tbi"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nextflow": "23.04.0"
         },
-        "timestamp": "2024-07-10T12:59:28.355632"
+        "timestamp": "2024-08-28T12:28:35.27599355"
     }
 }