Merge pull request #151 from drpatelh/bedtools

Follow up fixes for bedtools modules added in #79

.github/workflows/pytest-workflow.yml

@@ -25,7 +25,7 @@ jobs:
       matrix:
         nxf_version: ['20.11.0-edge']
         tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
-        profile: ['docker', 'singularity'] ## 'conda'
+        profile: ['docker', 'singularity', 'conda']
     env:
       NXF_ANSI_LOG: false
     steps:

software/bedtools/complement/main.nf

@@ -11,7 +11,7 @@ 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=2.30.0" : null)
+    conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
     } else {
@@ -19,10 +19,11 @@ process BEDTOOLS_COMPLEMENT {
     }
 
     input:
-    tuple val(meta), path(beds), path(sizes)
+    tuple val(meta), path(bed)
+    path  sizes
 
     output:
-    tuple val(meta), path('*.complement.bed'), emit: bed
+    tuple val(meta), path('*.bed'), emit: bed
     path  '*.version.txt'         , emit: version
 
     script:
@@ -31,10 +32,10 @@ process BEDTOOLS_COMPLEMENT {
     """
     bedtools \\
         complement \\
-        -i $beds \\
+        -i $bed \\
         -g $sizes \\
         $options.args \\
-        > ${prefix}.complement.bed
+        > ${prefix}.bed
 
     bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
     """

software/bedtools/complement/meta.yml

@@ -24,22 +24,25 @@ params:
         description: |
             Run the module with Conda using the software specified
             via the `conda` directive
-
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
         description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-    - beds:
+    - bed:
         type: file
-        description: List of bed files
+        description: Input BED file
         pattern: "*.{bed}"
     - sizes:
         type: file
         description: File which defines the chromosome lengths for a given genome
         pattern: "*.{sizes}"
-
 output:
     - meta:
         type: map
@@ -49,7 +52,7 @@ output:
     - bed:
         type: file
         description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
-        pattern: "*.{complement.bed}"
+        pattern: "*.{bed}"
     - version:
         type: file
         description: File containing software version
@@ -57,3 +60,4 @@ output:
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"
+    - "@drpatelh"

software/bedtools/genomecov/main.nf

@@ -11,7 +11,7 @@ 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=2.30.0" : null)
+    conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
     } else {
@@ -19,10 +19,10 @@ process BEDTOOLS_GENOMECOV {
     }
 
     input:
-    tuple val(meta), path(bams)
+    tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("*.bed"), emit: coverage
+    tuple val(meta), path("*.bed"), emit: bed
     path  "*.version.txt"         , emit: version
 
     script:
@@ -31,7 +31,7 @@ process BEDTOOLS_GENOMECOV {
     """
     bedtools \\
         genomecov \\
-        -ibam $bams \\
+        -ibam $bam \\
         $options.args \\
         > ${prefix}.bed
 

software/bedtools/genomecov/meta.yml

@@ -9,7 +9,6 @@ tools:
         description: |
             A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
         documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
-
 params:
     - outdir:
         type: string
@@ -26,7 +25,11 @@ params:
         description: |
             Run the module with Conda using the software specified
             via the `conda` directive
-
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
@@ -35,7 +38,7 @@ input:
             e.g. [ id:'test', single_end:false ]
     - bam:
         type: file
-        description: List of bam files
+        description: Input BAM file
         pattern: "*.{bam}"
 output:
     - meta:
@@ -47,12 +50,11 @@ output:
         type: file
         description: Computed genomecov bed file
         pattern: "*.{bed}"
-
     - version:
         type: file
         description: File containing software version
         pattern: "*.{version.txt}"
-
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"
+    - "@drpatelh"

software/bedtools/intersect/main.nf

@@ -11,7 +11,7 @@ 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=2.30.0" : null)
+    conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
     } else {
@@ -22,7 +22,7 @@ process BEDTOOLS_INTERSECT {
     tuple val(meta), path(bed1), path(bed2)
 
     output:
-    tuple val(meta), path('*.intersect.bed'), emit: bed
+    tuple val(meta), path('*.bed'), emit: bed
     path  '*.version.txt'         , emit: version
 
     script:
@@ -31,10 +31,10 @@ process BEDTOOLS_INTERSECT {
     """
     bedtools \\
         intersect \\
-        -a ${bed1} \\
-        -b ${bed2} \\
+        -a $bed1 \\
+        -b $bed2 \\
         $options.args \\
-        > ${prefix}.intersect.bed
+        > ${prefix}.bed
 
     bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
     """

software/bedtools/intersect/meta.yml

@@ -24,7 +24,11 @@ params:
         description: |
             Run the module with Conda using the software specified
             via the `conda` directive
-
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
@@ -33,13 +37,12 @@ input:
             e.g. [ id:'test', single_end:false ]
     - bed1:
         type: file
-        description: Bed file, each feature in 1 is compared to 2 in search of overlaps
+        description: BED file, each feature in 1 is compared to 2 in search of overlaps
         pattern: "*.{bed}"
     - bed2:
         type: file
-        description: Second bed file, used to compare to 1.
+        description: Second bed file, used to compare to first BED file
         pattern: "*.{bed}"
-
 output:
     - meta:
         type: map
@@ -48,8 +51,8 @@ output:
             e.g. [ id:'test', single_end:false ]
     - bed:
         type: file
-        description: Overlapped bed file
-        pattern: "*.{intersect.bed}"
+        description: BED file with intersected intervals
+        pattern: "*.{bed}"
     - version:
         type: file
         description: File containing software version
@@ -57,3 +60,4 @@ output:
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"
+    - "@drpatelh"

software/bedtools/merge/main.nf

@@ -9,9 +9,9 @@ process BEDTOOLS_MERGE {
     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:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
+    conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
     } else {
@@ -19,10 +19,10 @@ process BEDTOOLS_MERGE {
     }
 
     input:
-    tuple val(meta), path(beds)
+    tuple val(meta), path(bed)
 
     output:
-    tuple val(meta), path('*.merged.bed'), emit: bed
+    tuple val(meta), path('*.bed'), emit: bed
     path  '*.version.txt'         , emit: version
 
     script:
@@ -31,9 +31,9 @@ process BEDTOOLS_MERGE {
     """
     bedtools \\
         merge \\
-        -i $beds \\
+        -i $bed \\
         $options.args \\
-        > ${prefix}.merged.bed
+        > ${prefix}.bed
 
     bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
     """

software/bedtools/merge/meta.yml

@@ -24,7 +24,11 @@ params:
         description: |
             Run the module with Conda using the software specified
             via the `conda` directive
-
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
@@ -33,9 +37,8 @@ input:
             e.g. [ id:'test', single_end:false ]
     - bed:
         type: file
-        description: Presorted interval bed file
+        description: Input BED file
         pattern: "*.{bed}"
-
 output:
     - meta:
         type: map
@@ -45,7 +48,7 @@ output:
     - bed:
         type: file
         description: Overlapped bed file with combined features
-        pattern: "*.{merged.bed}"
+        pattern: "*.{bed}"
     - version:
         type: file
         description: File containing software version
@@ -53,3 +56,4 @@ output:
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"
+    - "@drpatelh"

software/bedtools/slop/main.nf

@@ -11,19 +11,19 @@ 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=2.30.0" : null)
+    conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
     } else {
         container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
     }
 
-
     input:
-    tuple val(meta), path(beds), path (sizes)
+    tuple val(meta), path(bed)
+    path  sizes
 
     output:
-    tuple val(meta), path("*.slop.bed"), emit: bed
+    tuple val(meta), path("*.bed"), emit: bed
     path  "*.version.txt"         , emit: version
 
     script:
@@ -32,10 +32,10 @@ process BEDTOOLS_SLOP {
     """
     bedtools \\
         slop \\
-        -i $beds \\
+        -i $bed \\
         -g $sizes \\
         $options.args \\
-        > ${prefix}.slop.bed
+        > ${prefix}.bed
 
     bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
     """

software/bedtools/slop/meta.yml

@@ -8,27 +8,7 @@ tools:
         description: |
             A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
         documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
-
 params:
-  - l:
-      type: integer
-      description: The number of base pairs to subtract from the start coordinate
-  - r:
-      type: integer
-      description: The number of base pairs to add to the end coordinate
-  - b:
-      type: integer
-      description: Increases the entry by the same number base pairs in each direction
-  - pct:
-      type: boolean
-      description: |
-        Define -l and -r as a fraction of the feature’s length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. By default this is set to false.
-
-  - header:
-      type: boolean
-      description: |
-        Print the header from the input file prior to results.
-
     - outdir:
         type: string
         description: |
@@ -44,7 +24,11 @@ params:
         description: |
             Run the module with Conda using the software specified
             via the `conda` directive
-
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
@@ -53,7 +37,7 @@ input:
             e.g. [ id:'test', single_end:false ]
     - bed:
         type: file
-      description: List of bed files
+        description: Input BED file
         pattern: "*.{bed}"
 output:
     - meta:
@@ -63,13 +47,13 @@ output:
             e.g. [ id:'test', single_end:false ]
     - bed:
         type: file
-      description: Edited bed file
-      pattern: "*.{slop.bed}"
-
+        description: Slopped BED file
+        pattern: "*.{bed}"
     - version:
         type: file
         description: File containing software version
         pattern: "*.{version.txt}"
-
-authors: -"@Emiller88"
+authors:
+    - "@Emiller88"
     - "@sruthipsuresh"
+    - "@drpatelh"

software/bedtools/sort/main.nf

@@ -11,7 +11,7 @@ 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=2.30.0" : null)
+    conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
     } else {
@@ -19,10 +19,10 @@ process BEDTOOLS_SORT {
     }
 
     input:
-    tuple val(meta), path(beds)
+    tuple val(meta), path(bed)
 
     output:
-    tuple val(meta), path('*.sort.bed'), emit: bed
+    tuple val(meta), path('*.bed'), emit: bed
     path  '*.version.txt'         , emit: version
 
     script:
@@ -31,9 +31,9 @@ process BEDTOOLS_SORT {
     """
     bedtools \\
         sort \\
-        -i $beds \\
+        -i $bed \\
         $options.args \\
-        > ${prefix}.sort.bed
+        > ${prefix}.bed
 
     bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
     """

software/bedtools/sort/meta.yml

@@ -24,18 +24,21 @@ params:
         description: |
             Run the module with Conda using the software specified
             via the `conda` directive
-
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
         description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-    - beds:
+    - bed:
         type: file
-        description: List of bed files
+        description: Input BED file
         pattern: "*.{bed}"
-
 output:
     - meta:
         type: map
@@ -44,14 +47,13 @@ output:
             e.g. [ id:'test', single_end:false ]
     - bed:
         type: file
-        description: Sorted bed file
-        pattern: "*.{sort.bed}"
-
+        description: Sorted BED file
+        pattern: "*.{bed}"
     - version:
         type: file
         description: File containing software version
         pattern: "*.{version.txt}"
-
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"
+    - "@drpatelh"

tests/software/bedtools/complement/main.nf

@@ -7,8 +7,7 @@ include { BEDTOOLS_COMPLEMENT } from '../../../../software/bedtools/complement/m
 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) ]
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
 
-    BEDTOOLS_COMPLEMENT( input )
+    BEDTOOLS_COMPLEMENT ( input, file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) )
 }

tests/software/bedtools/complement/test.yml

@@ -4,5 +4,5 @@
     - bedtools
     - bedtools_complement
   files:
-    - path: output/bedtools/test.complement.bed
+    - path: output/bedtools/test.bed
       md5sum: 55a43973abb1a08ac57290ff44f6c502

tests/software/bedtools/genomecov/main.nf

@@ -4,7 +4,6 @@ nextflow.enable.dsl = 2
 
 include { BEDTOOLS_GENOMECOV } from '../../../../software/bedtools/genomecov/main.nf' addParams( options: [:] )
 
-
 workflow test_bedtools_genomecov {
     def input = []
     input = [ [ id:'test'],

tests/software/bedtools/intersect/test.yml

@@ -4,5 +4,5 @@
     - bedtools
     - bedtools_intersect
   files:
-    - path: output/bedtools/test.intersect.bed
+    - path: output/bedtools/test.bed
       md5sum: cc1bb317886e7df0a942b56f8a320d9c

tests/software/bedtools/merge/test.yml

@@ -4,5 +4,5 @@
     - bedtools
     - bedtools_merge
   files:
-    - path: output/bedtools/test.merged.bed
+    - path: output/bedtools/test.bed
       md5sum: 13e5a3b254fac35fe0da0c92cbaf1761

tests/software/bedtools/slop/main.nf

@@ -7,9 +7,8 @@ include { BEDTOOLS_SLOP } from '../../../../software/bedtools/slop/main.nf' addP
 workflow test_bedtools_slop {
     def input = []
     input = [ [ id:'test'],
-              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
-              file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ]
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
 
-    BEDTOOLS_SLOP( input )
+    BEDTOOLS_SLOP ( input, file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) )
 }
 

tests/software/bedtools/slop/test.yml

@@ -4,5 +4,5 @@
     - bedtools
     - bedtools_slop
   files:
-    - path: output/bedtools/test.slop.bed
+    - path: output/bedtools/test.bed
       md5sum: 5f6ecc3e3cc6cee9537a1d088b02abec

tests/software/bedtools/sort/main.nf

@@ -10,5 +10,4 @@ workflow test_bedtools_sort {
               file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
 
     BEDTOOLS_SORT ( input )
-
 }

tests/software/bedtools/sort/test.yml

@@ -4,5 +4,5 @@
     - bedtools
     - bedtools_sort
   files:
-    - path: output/bedtools/test.sort.bed
+    - path: output/bedtools/test.bed
       md5sum: 4279202e33fcce3d19f420f1b27fddee