Add new module: samtools/consensus (nf-core#6064)

* Add new module: samtools/consensus * Update modules/nf-core/samtools/consensus/main.nf Co-authored-by: Simon Pearce <[email protected]> * add thread option * Add more test modes to the test * Update modules/nf-core/samtools/consensus/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/samtools/consensus/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/samtools/consensus/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/samtools/consensus/main.nf Co-authored-by: Simon Pearce <[email protected]> * update snapshot of the test --------- Co-authored-by: Simon Pearce <[email protected]>
genomic-medicine-sweden · Jul 31, 2024 · 4133cae · 4133cae
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diff --git a/modules/nf-core/samtools/consensus/environment.yml b/modules/nf-core/samtools/consensus/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "samtools_consensus"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::samtools=1.20"
diff --git a/modules/nf-core/samtools/consensus/main.nf b/modules/nf-core/samtools/consensus/main.nf
@@ -0,0 +1,60 @@
+process SAMTOOLS_CONSENSUS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_1':
+        'biocontainers/samtools:1.20--h50ea8bc_1' }"
+
+    input:
+    tuple val(meta), path(input)
+
+    output:
+    tuple val(meta), path("*.fasta") , emit: fasta , optional: true
+    tuple val(meta), path("*.fastq") , emit: fastq , optional: true
+    tuple val(meta), path("*.pileup"), emit: pileup, optional: true
+    path "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("-f fastq") ? "fastq" :
+                    args.contains("-f pileup") ? "pileup" :
+                    args.contains("-f fasta") ? "fasta" :
+                    "fasta"
+
+    """
+    samtools \\
+        consensus \\
+        $args \\
+        -@ $task.cpus \\
+        -o ${prefix}.${extension} \\
+        $input
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(samtools --version |& sed '1!d ; s/samtools //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("-f fastq") ? "fastq" :
+                    args.contains("-f pileup") ? "pileup" :
+                    args.contains("-f fasta") ? "fasta" :
+                    "fasta"
+
+    """
+    touch ${prefix}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(samtools --version |& sed '1!d ; s/samtools //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/samtools/consensus/meta.yml b/modules/nf-core/samtools/consensus/meta.yml
@@ -0,0 +1,54 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "samtools_consensus"
+description: Produces a consensus FASTA/FASTQ/PILEUP
+keywords:
+  - consensus
+  - bam
+  - fastq
+  - fasta
+  - pileup
+tools:
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: http://www.htslib.org/doc/samtools.html
+      tool_dev_url: "https://github.com/samtools/samtools"
+      doi: "10.1093/bioinformatics/btp352"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - input:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - output:
+      type: file
+      description: Consensus sequences
+      pattern: "*.{fasta,fastq,pileup}"
+
+authors:
+  - "@LilyAnderssonLee"
+maintainers:
+  - "@LilyAnderssonLee"
diff --git a/modules/nf-core/samtools/consensus/tests/fastq.config b/modules/nf-core/samtools/consensus/tests/fastq.config
@@ -0,0 +1,5 @@
+process {
+    withName: SAMTOOLS_CONSENSUS {
+        ext.args2 = '-f fastq'
+    }
+}
diff --git a/modules/nf-core/samtools/consensus/tests/main.nf.test b/modules/nf-core/samtools/consensus/tests/main.nf.test
@@ -0,0 +1,106 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_CONSENSUS"
+    script "../main.nf"
+    process "SAMTOOLS_CONSENSUS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/consensus"
+
+    test("sarscov2 - bam - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    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.bai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+    test("sarscov2 - bam - fastq") {
+
+        config "./fastq.config"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    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.bai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+    test("sarscov2 - bam - pileup") {
+
+        config "./pileup.config"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    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.bai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    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.bai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}