Samtools mpileup input update

modules/nf-core/poolsnp/tests/main.nf.test

@@ -17,10 +17,17 @@ nextflow_process {
             """
             input[0] = [
                 [ id:'test'],
-                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
             ]
             input[1] = [
+                [ ],
+                [ ]
+            ]
+            input[2] = [
+                [ id: 'test'],
+                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+            ]
+            input[3] = [
                 [ id: 'fasta'],
                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
             ]

modules/nf-core/samtools/mpileup/environment.yml

@@ -5,6 +5,6 @@ channels:
   - bioconda
 dependencies:
   # renovate: datasource=conda depName=bioconda/htslib
-  - bioconda::htslib=1.22.1
+  - bioconda::htslib=1.23
   # renovate: datasource=conda depName=bioconda/samtools
-  - bioconda::samtools=1.22.1
+  - bioconda::samtools=1.23

modules/nf-core/samtools/mpileup/main.nf

@@ -4,16 +4,18 @@ process SAMTOOLS_MPILEUP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' :
-        'biocontainers/samtools:1.22.1--h96c455f_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.23--h96c455f_0' :
+        'biocontainers/samtools:1.23--h96c455f_0' }"
 
     input:
-    tuple val(meta), path(input), path(intervals)
-    tuple val(meta2), path(fasta)
+    tuple val(meta), path(input)       // sam/bam/cram
+    tuple val(meta), path(index)       // csi/bai/crai - optional, only required when using '-r'
+    tuple val(meta), path(intervals)   // optional
+    tuple val(meta2), path(fasta)      // optional
 
     output:
     tuple val(meta), path("*.mpileup.gz"), emit: mpileup
-    tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -1 | sed -e "s/samtools //"'), emit: versions_samtools, topic: versions
+    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), emit: versions_samtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/samtools/mpileup/meta.yml

@@ -1,5 +1,6 @@
 name: samtools_mpileup
-description: Generate text pileup output for one or multiple BAM files. Each input file produces a separate group of pileup columns in the output.
+description: Generate text pileup output for one or multiple BAM files. Each
+  input file produces a separate group of pileup columns in the output.
 keywords:
   - mpileup
   - bam
@@ -27,19 +28,35 @@ input:
         description: BAM/CRAM/SAM file
         pattern: "*.{bam,cram,sam}"
         ontologies: []
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - index:
+        type: file
+        description: CSI/BAI/CRAI file. Optional. Only required when using the
+          '-r' parameter.
+        pattern: "*.{bam,cram,sam}"
+        ontologies: []
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
     - intervals:
         type: file
-        description: Interval FILE
+        description: Interval FILE. Optional.
         pattern: "*.bed"
         ontologies: []
   - - meta2:
         type: map
         description: |
-          Groovy Map containing sample information
+          Groovy Map containing reference information
           e.g. [ id:'test' ]
     - fasta:
         type: file
-        description: FASTA reference file
+        description: FASTA reference file. Optional.
         pattern: "*.{fasta,fa}"
         ontologies: []
 output:
@@ -57,28 +74,27 @@ output:
   versions_samtools:
     - - ${task.process}:
           type: string
-          description: Name of the process
+          description: The process the versions were collected from
       - samtools:
           type: string
-          description: Name of the tool
-      - samtools --version | head -1 | sed -e "s/samtools //":
-          type: eval
-          description: The expression to obtain the version of the tool
-
+          description: The tool name
+      - "samtools version | sed '1!d;s/.* //'":
+          type: string
+          description: The command used to generate the version of the tool
 topics:
   versions:
     - - ${task.process}:
           type: string
-          description: Name of the process
+          description: The process the versions were collected from
       - samtools:
           type: string
-          description: Name of the tool
-      - samtools --version | head -1 | sed -e "s/samtools //":
-          type: eval
-          description: The expression to obtain the version of the tool
-
+          description: The tool name
+      - "samtools version | sed '1!d;s/.* //'":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@drpatelh"
   - "@joseespinosa"
 maintainers:
   - "@joseespinosa"
+  - "@krannich479"

modules/nf-core/samtools/mpileup/tests/main.nf.test

@@ -9,17 +9,18 @@ nextflow_process {
     tag "samtools"
     tag "samtools/mpileup"
 
-    test("bam_bed") {
+    test("bam - no fasta") {
 
         when {
             process {
                 """
                 input[0] = [
                     [ id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    []
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
                 ]
                 input[1] = [[],[]]
+                input[2] = [[],[]]
+                input[3] = [[],[]]
                 """
             }
         }
@@ -32,17 +33,18 @@ nextflow_process {
         }
     }
 
-    test("bam_bed_fasta") {
+    test("bam - fasta") {
 
         when {
             process {
                 """
                 input[0] = [
                     [ id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    []
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
                 ]
-                input[1] = [
+                input[1] = [[],[]]
+                input[2] = [[],[]]
+                input[3] = [
                     [ id: 'fasta'],
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
@@ -58,17 +60,50 @@ nextflow_process {
         }
     }
 
-    test("bam_bed --stub") {
+    test("bam - region - bai") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                module_args     = "-r MT192765.1"
+                module_prefix   = "test"
+            }
+            process {                
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[2] = [[],[]]
+                input[3] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match()}
+            )
+        }
+    }
+
+    test("bam - stub") {
         options '-stub'
         when {
             process {
                 """
                 input[0] = [
                     [ id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    []
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
                 ]
                 input[1] = [[],[]]
+                input[2] = [[],[]]
+                input[3] = [[],[]]
                 """
             }
         }