rebased and updated all bedtools testing and modules

.github/workflows/bedtools_complement

@@ -0,0 +1,40 @@
+name: bedtools_complement
+on:
+  push:
+    paths:
+      - software/bedtools/complement/**
+      - .github/workflows/bedtools_complement.yml
+      - tests/software/bedtools/**
+  pull_request:
+    paths:
+      - software/bedtools/complement/**
+      - .github/workflows/bedtools_complement.yml
+      - tests/software/bedtools/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag bedtools_complement --symlink --wt 2

.github/workflows/bedtools_genomecov

@@ -0,0 +1,40 @@
+name: bedtools_genomecov
+on:
+  push:
+    paths:
+      - software/bedtools/genomecov/**
+      - .github/workflows/bedtools_genomecov.yml
+      - tests/software/bedtools/**
+  pull_request:
+    paths:
+      - software/bedtools/genomecov/**
+      - .github/workflows/bedtools_genomecov.yml
+      - tests/software/bedtools/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag bedtools_genomecov --symlink --wt 2

.github/workflows/bedtools_intersect

@@ -0,0 +1,40 @@
+name: bedtools_intersect
+on:
+  push:
+    paths:
+      - software/bedtools/intersect/**
+      - .github/workflows/bedtools_intersect.yml
+      - tests/software/bedtools/**
+  pull_request:
+    paths:
+      - software/bedtools/intersect/**
+      - .github/workflows/bedtools_intersect.yml
+      - tests/software/bedtools/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag bedtools_intersect --symlink --wt 2

.github/workflows/bedtools_merge

@@ -0,0 +1,40 @@
+name: bedtools_merge
+on:
+  push:
+    paths:
+      - software/bedtools/merge/**
+      - .github/workflows/bedtools_merge.yml
+      - tests/software/bedtools/**
+  pull_request:
+    paths:
+      - software/bedtools/merge/**
+      - .github/workflows/bedtools_merge.yml
+      - tests/software/bedtools/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag bedtools_merge--symlink --wt 2

.github/workflows/bedtools_slop

@@ -0,0 +1,40 @@
+name: bedtools_slop
+on:
+  push:
+    paths:
+      - software/bedtools/slop/**
+      - .github/workflows/bedtools_slop.yml
+      - tests/software/bedtools/**
+  pull_request:
+    paths:
+      - software/bedtools/slop/**
+      - .github/workflows/bedtools_slop.yml
+      - tests/software/bedtools/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag bedtools_slop--symlink --wt 2

.github/workflows/bedtools_sort

@@ -0,0 +1,40 @@
+name: bedtools_sort
+on:
+  push:
+    paths:
+      - software/bedtools/sort/**
+      - .github/workflows/bedtools_sort.yml
+      - tests/software/bedtools/**
+  pull_request:
+    paths:
+      - software/bedtools/sort/**
+      - .github/workflows/bedtools_sort.yml
+      - tests/software/bedtools/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag bedtools_sort--symlink --wt 2

software/bedtools/complement/main.nf

@@ -10,12 +10,15 @@ process BEDTOOLS_COMPLEMENT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda     (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
+    } else {
     container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
+    }
     
     input:
-        tuple val(meta), path(beds)
+        tuple val(meta), path(beds), path (sizes)
-        path  sizes
 
     output:
         tuple val(meta), path("*.complement.bed"), emit: complement

software/bedtools/genomecov/functions.nf

@@ -22,7 +22,6 @@ def initOptions(Map args) {
     options.publish_dir   = args.publish_dir ?: ''
     options.publish_files = args.publish_files
     options.suffix        = args.suffix ?: ''
-    options.sizeA         - args.sizeA ?: '-sizeA'
     return options
 }
 

software/bedtools/genomecov/main.nf

@@ -10,12 +10,15 @@ process BEDTOOLS_GENOMECOV {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda     (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
+    } else {
     container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
+    }
 
     input:
-        tuple val(meta), path(bams)
+        tuple val(meta), path(bams), path (sizes)
-        path sizes
 
     output:
         tuple val(meta), path("*.bed"), emit: coverage

software/bedtools/intersect/main.nf

@@ -10,12 +10,15 @@ process BEDTOOLS_INTERSECT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
     
-    conda     (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
+    } else {
     container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
+    }
 
     input:
-        tuple val(meta), path(beds)
+        tuple val(meta), path(bedfile1), path(bedfile2)
-
     output:
         tuple val(meta), path("*.intersect.bed"), emit: intersect
         path  "*.version.txt", emit: version
@@ -24,7 +27,7 @@ process BEDTOOLS_INTERSECT {
         def software = getSoftwareName(task.process)
         def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
         """
-        bedtools intersect -a ${beds[0]} -b ${beds[1]} ${options.args} > ${prefix}.intersect.bed
+        bedtools intersect -a ${bedfile1} -b ${bedfile2} ${options.args} > ${prefix}.intersect.bed
         bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
         """
 }

software/bedtools/merge/main.nf

@@ -4,27 +4,28 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 def options    = initOptions(params.options)
 
 process BEDTOOLS_MERGE {
-    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), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda     (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
+    } else {
     container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
-
+    }
     input:
-        tuple val(meta), path(beds)
+        path(sort)
 
     output:
-        tuple val(meta), path("*.merged.bed"), emit: merge
+        path("*.merged.bed"), emit: merge
         path  "*.version.txt", emit: version
-
+// TODO fix output file naming
     script:
         def software = getSoftwareName(task.process)
-        def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
         """
-        bedtools merge -i $beds ${options.args} > ${prefix}.merged.bed
+        bedtools merge -i $sort ${options.args} > test.merged.bed 
         bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
         """
 }

software/bedtools/slop/main.nf

@@ -10,13 +10,16 @@ process BEDTOOLS_SLOP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda     (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
+    } else {
     container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
+    }
     
 
     input:
-        tuple val(meta), path(beds)
+        tuple val(meta), path(beds), path (sizes)
-        path  sizes
 
     output:
         tuple val(meta), path("*.slop.bed"), emit: slopbed

software/bedtools/sort/main.nf

@@ -10,21 +10,25 @@ process BEDTOOLS_SORT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda     (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"
+    } else {
     container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
+    }
 
     input:
         tuple val(meta), path(beds)
 
     output:
-        tuple val(meta), path("*.sort.bed"), emit: sort
+        tuple val(meta), path("*.sort"), emit: sort
         path  "*.version.txt", emit: version
 
     script:
         def software = getSoftwareName(task.process)
         def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
         """
-        bedtools sort -i $beds ${options.args} > ${prefix}.sort.bed
+        bedtools sort -i $beds ${options.args} > ${prefix}.sort
         bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
         """
 }

tests/software/bedtools/main.nf

@@ -0,0 +1,88 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_COMPLEMENT } from '../../../software/bedtools/complement/main.nf' addParams( options: [:] )
+include { BEDTOOLS_GENOMECOV } from '../../../software/bedtools/genomecov/main.nf' addParams( options: [:] )
+include { BEDTOOLS_INTERSECT } from '../../../software/bedtools/intersect/main.nf' addParams( options: [:] )
+include { BEDTOOLS_MERGE } from '../../../software/bedtools/merge/main.nf' addParams( options: [:] )
+include { BEDTOOLS_SLOP as BEDTOOLS_SLOP_S} from '../../../software/bedtools/slop/main.nf' addParams( options: [:] )
+include { BEDTOOLS_SLOP as BEDTOOLS_SLOP_AS} from '../../../software/bedtools/slop/main.nf' addParams( options: [:] )
+include { BEDTOOLS_SORT } from '../../../software/bedtools/sort/main.nf' addParams( options: [publish_dir: 'test_bedtools_sort'] ) // needed for merge
+
+
+workflow test_bedtools_complement {
+    def input = []
+    input = [ [ id:'test'], 
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
+              file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
+
+    BEDTOOLS_COMPLEMENT( input )
+}
+
+workflow test_bedtools_genomecov {
+    def input = []
+    input = [ [ id:'test'], 
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
+              file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
+
+    BEDTOOLS_GENOMECOV( input )
+}
+
+workflow test_bedtools_intersect {
+    def input = []
+    input = [ [ id:'test'], 
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
+              file("${launchDir}/tests/data/bed/B.bed", checkIfExists: true) ] //metamap
+
+    BEDTOOLS_INTERSECT( input )
+}
+
+
+//  ensure input file is presorted (uses output of sort module)
+workflow test_bedtools_merge {
+    test_bedtools_sort()
+    def input = []
+    input = [ 
+        test_bedtools_sort.out.sort.collect { it[1] }.ifEmpty([]) 
+    ]
+    BEDTOOLS_MERGE(*input)
+}
+
+// TODO streamline slop module
+
+// To run with header and pct enabled, type --pct true and --header true with nextflow run command. 
+/*
+Test with l/r method
+*/
+workflow test_bedtools_slop_asymmetrical {
+    def input = []
+    input = [ [ id:'test', symmetry: false], 
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
+              file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
+    BEDTOOLS_SLOP_AS( input )
+}
+/*
+Test with b method
+*/
+workflow test_bedtools_slop_symmetrical {
+    def input = []
+    input = [ [ id:'test', symmetry: true], 
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
+              file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
+    BEDTOOLS_SLOP_S( input )
+}
+
+workflow test_bedtools_sort {
+    def input = []
+    input = [ [ id:'test'], 
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
+
+    BEDTOOLS_SORT( input )
+    
+    emit:
+    sort = BEDTOOLS_SORT.out.sort
+
+}
+
+

tests/software/bedtools/test.yml

@@ -0,0 +1,67 @@
+- name: Run bedtools complement test workflow
+  command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_complement -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_complement
+  files:
+    - path: output/bedtools/test.complement.bed
+      md5sum: 55a43973abb1a08ac57290ff44f6c502
+
+- name: Run bedtools genomecov test workflow
+  command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_genomecov -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_genomecov
+  files:
+    - path: output/bedtools/test.bed
+      md5sum: 5be12e847b933b02bf42437e8562d06c
+
+- name: Run bedtools intersect test workflow
+  command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_intersect -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_intersect
+  files:
+    - path: output/bedtools/test.intersect.bed
+      md5sum: cc1bb317886e7df0a942b56f8a320d9c
+
+      
+- name: Run bedtools sort test workflow
+  command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_sort -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_sort
+  files:
+    - path: output/bedtools/test.sort.bed
+      md5sum: 4279202e33fcce3d19f420f1b27fddee
+
+# linked to sort module
+- name: Run bedtools merge test workflow
+  command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_merge -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_merge
+  files:
+    - path: output/bedtools/test.merged.bed
+      md5sum: 13e5a3b254fac35fe0da0c92cbaf1761
+
+- name: Run bedtools slop test workflow (symmetrical)
+  command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_slop_symmetrical -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_slop
+  files:
+    - path: output/bedtools/test.slop.bed
+      md5sum: 4279202e33fcce3d19f420f1b27fddee
+
+- name: Run bedtools slop test workflow (asymmetrical)
+  command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_slop_asymmetrical -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_slop
+  files:
+    - path: output/bedtools/test.slop.bed
+      md5sum: 4279202e33fcce3d19f420f1b27fddee
+
+
+