Add meta to bowtie build

modules/nf-core/bowtie/align/main.nf

@@ -9,13 +9,13 @@ process BOWTIE_ALIGN {
 
     input:
     tuple val(meta), path(reads)
-    path  index
+    tuple val(meta2), path(index)
 
     output:
-    tuple val(meta), path('*.bam'), emit: bam
-    tuple val(meta), path('*.out'), emit: log
-    path  "versions.yml"          , emit: versions
-    tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
+    tuple val(meta), path('*.bam')     , emit: bam
+    tuple val(meta), path('*.out')     , emit: log
+    tuple val(meta), path('*fastq.gz') , emit: fastq, optional : true
+    path  "versions.yml"               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -53,4 +53,24 @@ process BOWTIE_ALIGN {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def unaligned = params.save_unaligned ?
+                    meta.single_end ? "echo '' | gzip > ${prefix}.unmapped.fastq.gz" :
+                                    "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz; echo '' | gzip > ${prefix}.unmapped_2.fastq.gz"
+                    : ''
+    """
+    touch ${prefix}.bam
+    touch ${prefix}.out
+    $unaligned
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bowtie: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+
 }

modules/nf-core/bowtie/align/meta.yml

@@ -27,6 +27,11 @@ input:
       description: |
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
         respectively.
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing genome information
+        e.g. [ id:'sarscov2' ]
   - index:
       type: file
       description: Bowtie genome index files
@@ -36,14 +41,19 @@ output:
       type: file
       description: Output BAM file containing read alignments
       pattern: "*.{bam}"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - fastq:
       type: file
       description: Unaligned FastQ files
       pattern: "*.fastq.gz"
+  - log:
+      type: file
+      description: Log file
+      pattern: "*.log"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
 authors:
   - "@kevinmenden"
 maintainers:

modules/nf-core/bowtie/align/tests/main.nf.test

@@ -0,0 +1,126 @@
+nextflow_process {
+
+    name "Test Process BOWTIE_ALIGN"
+    script "../main.nf"
+    process "BOWTIE_ALIGN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bowtie"
+    tag "bowtie/align"
+    tag "bowtie/build"
+
+
+    setup {
+        run("BOWTIE_BUILD") {
+            script "../../../bowtie/build/main.nf"
+            process {
+                """
+                input[0] = [[ id:'sarscov2' ],
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - single_end") {
+
+        when {
+            process {
+                """
+                input[0] = [ [id:"test", single_end:true],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                input[1] = BOWTIE_BUILD.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions,
+                                  process.out.bam.collect { bam(it[1]).getHeaderMD5() },
+                                  process.out.bam.collect { bam(it[1]).getReadsMD5() },
+                                  process.out.log
+                                  ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - single_end - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [id:"test", single_end:true],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                input[1] = BOWTIE_BUILD.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - paired_end") {
+
+        when {
+            process {
+                """
+                input[0] = [ [id:"test", single_end:false],
+                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                    ]
+                input[1] = BOWTIE_BUILD.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions,
+                                  process.out.bam.collect { bam(it[1]).getHeaderMD5() },
+                                  process.out.bam.collect { bam(it[1]).getReadsMD5() },
+                                  process.out.log
+                                  ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - paired_end - stub") {
+
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [ [id:"test", single_end:false],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                input[1] = BOWTIE_BUILD.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}