Add samtools ampliconclip (#590)

* created template for `samtools/ampliconclip` (#584)

* All tests passing (#584)

* Linting fixed (#584)

* Final linting fixed (#584)

* Optional output flags moved to `input` (#584)

* typo fix (#584)

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/samtools/ampliconclip/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

modules/samtools/ampliconclip/main.nf

@@ -0,0 +1,51 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process SAMTOOLS_AMPLICONCLIP {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::samtools=1.13" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
+    } else {
+        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+    path bed
+    val save_cliprejects
+    val save_clipstats
+
+    output:
+    tuple val(meta), path("*.bam")            , emit: bam
+    tuple val(meta), path("*.clipstats.txt")  , optional:true, emit: stats
+    tuple val(meta), path("*.cliprejects.bam"), optional:true, emit: rejects_bam
+    path "*.version.txt"                      , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def rejects  = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
+    def stats    = save_clipstats   ? "-f ${prefix}.clipstats.txt"               : ""
+    """
+    samtools \\
+        ampliconclip \\
+        $options.args \\
+        -@ $task.cpus \\
+        $rejects \\
+        $stats \\
+        -b $bed \\
+        -o ${prefix}.bam \\
+        $bam
+
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}

modules/samtools/ampliconclip/meta.yml

@@ -0,0 +1,64 @@
+name: samtools_ampliconclip
+description: write your description here
+keywords:
+  - amplicon
+  - clipping
+  - ampliconclip
+  - samtools ampliconclip
+  - samtools
+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: hhttp://www.htslib.org/doc/samtools.html
+        doi: 10.1093/bioinformatics/btp352
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - bed:
+      type: file
+      description: BED file of regions to be removed (e.g. amplicon primers)
+      pattern: "*.{bed}"
+  - save_cliprejects:
+      type: value
+      description: Save filtered reads to a file
+  - save_clipstats:
+      type: value
+      description: Save clipping stats to a file
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - bam:
+      type: file
+      description: Clipped reads BAM file
+      pattern: "*.{bam}"
+  - stats:
+      type: file
+      description: Clipping statistics text file
+      pattern: "*.{clipstats.txt}"
+  - rejects_bam:
+      type: file
+      description: Filtered reads BAM file
+      pattern: "*.{cliprejects.bam}"
+
+authors:
+  - "@bjohnnyd"

tests/config/pytest_modules.yml

@@ -651,6 +651,10 @@ salmon/quant:
   - modules/salmon/quant/**
   - tests/modules/salmon/quant/**
 
+samtools/ampliconclip:
+  - modules/samtools/ampliconclip/**
+  - tests/modules/samtools/ampliconclip/**
+
 samtools/faidx:
   - modules/samtools/faidx/**
   - tests/modules/samtools/faidx/**

tests/modules/samtools/ampliconclip/main.nf

@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_AMPLICONCLIP } from '../../../../modules/samtools/ampliconclip/main.nf' addParams([:])
+
+workflow test_samtools_ampliconclip_no_stats_no_rejects {
+
+    input = [ 
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    save_cliprejects = false
+    save_clipstats   = false
+
+    SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
+}
+
+workflow test_samtools_ampliconclip_no_stats_with_rejects {
+
+    input = [ 
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    save_cliprejects = true
+    save_clipstats   = false
+
+    SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
+}
+
+workflow test_samtools_ampliconclip_with_stats_with_rejects {
+
+    input = [ 
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    save_cliprejects = true
+    save_clipstats   = true
+
+    SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
+}

tests/modules/samtools/ampliconclip/test.yml

@@ -0,0 +1,34 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml samtools/ampliconclip
+- name: samtools ampliconclip no stats no rejects
+  command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_no_rejects -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/ampliconclip
+  files:
+    - path: output/samtools/test.bam
+      md5sum: 1c705ebe39f68f1dac164733ae99c9d2
+
+- name: samtools ampliconclip no stats with rejects
+  command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/ampliconclip
+  files:
+    - path: output/samtools/test.bam
+      md5sum: 86c7bfb5378d57b16855c5b399000b2a
+    - path: output/samtools/test.cliprejects.bam
+      md5sum: 8e2eea2c0005b4d4e77c0eb549599133
+
+- name: samtools ampliconclip with stats with rejects
+  command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/ampliconclip
+  files:
+    - path: output/samtools/test.bam
+      md5sum: d96f5eebef0ff4635e68090e89756d4a
+    - path: output/samtools/test.cliprejects.bam
+      md5sum: ad83a523d6ff1c58caade4ddafbaaed7
+    - path: output/samtools/test.clipstats.txt
+      md5sum: 6fbde83d658cd2813b79900d33800d1d