feat: add bedops/bedmap module

CHANGELOG.md

@@ -4,6 +4,7 @@ Our documentation website is now live: <https://ccbr.github.io/nf-modules/> (#16
 
 ### New modules
 
+- bedops/bedmap (#37)
 - bedtools/map (#37)
 - bedtools/merge (#37)
 - bedtools/sort (#37)

modules/CCBR/bedops/bedmap/main.nf

@@ -0,0 +1,37 @@
+process BEDOPS_BEDMAP {
+    tag { meta.id }
+    label 'process_single'
+    container 'nciccbr/ccbr_ubuntu_base_20.04:v6.1'
+
+    input:
+    tuple val(meta1), path(refbed)
+    tuple val(meta2), path(mapbed)
+
+    output:
+    tuple val(meta2), path("*.mapped.bed"), emit: bed
+    path "versions.yml"                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+    bedmap \\
+        --delim '\t' \\
+        --echo-ref-name \\
+        --count \\
+        ${refbed} \\
+        ${mapbed} \\
+        > ${meta2.id}.mapped.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedops: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${meta2.id}.mapped.bed versions.yml
+    """
+}

modules/CCBR/bedops/bedmap/meta.yml

@@ -0,0 +1,55 @@
+---
+name: "bedops_bedmap"
+description: The bedmap program is used to retrieve and process signal or other features over regions of interest in BED files
+keywords:
+  - bedops
+  - bedmap
+  - bed
+  - intervals
+tools:
+  - bedops:
+      description: |
+        fast, highly scalable and easily-parallelizable genome analysis toolkit
+      documentation: https://bedops.readthedocs.io/
+      tool_dev_url: https://github.com/bedops/bedops
+      licence: ["GPLv2"]
+      doi: 10.1093/bioinformatics/bts277
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - refbed:
+      type: file
+      description: BED file
+      pattern: "*.bed"
+  - mapbed:
+      type: file
+      description: BED file
+      pattern: "*.bed"
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - mapped_bed:
+      type: file
+      description: BED file
+      pattern: "*.bed"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@kelly-sovacool"
+maintainers:
+  - "@kelly-sovacool"

tests/config/pytest_modules.yml

@@ -1,3 +1,7 @@
+bedops/bedmap:
+  - modules/CCBR/bedops/bedmap/**
+  - tests/modules/CCBR/bedops/bedmap/**
+
 bedtools/map:
   - modules/CCBR/bedtools/map/**
   - tests/modules/CCBR/bedtools/map/**

tests/modules/CCBR/bedops/bedmap/main.nf

@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CAT_CAT                    } from '../../../../../modules/CCBR/cat/cat/main.nf'
+include { BEDOPS_BEDMAP              } from '../../../../../modules/CCBR/bedops/bedmap/main.nf'
+include { BEDTOOLS_SORT as SORT_CAT
+          BEDTOOLS_SORT as SORT_PEAK } from '../../../../../modules/CCBR/bedtools/sort/main.nf'
+include { BEDTOOLS_MERGE             } from '../../../../../modules/CCBR/bedtools/merge/main.nf'
+
+workflow test_bedops_bedmap {
+
+    ch_peaks = [
+        [ id: 'test', group: 'macs_broad' ], // meta map
+        [ file(params.test_data['macs_peaks_1'], checkIfExists: true),
+          file(params.test_data['macs_peaks_2'], checkIfExists: true),
+        ]
+    ]
+
+    ch_peaks.collect() | CAT_CAT
+    CAT_CAT.out.file_out | SORT_CAT
+    SORT_CAT.out.sorted | BEDTOOLS_MERGE
+
+    ch_peaks | SORT_PEAK
+    BEDOPS_BEDMAP( BEDTOOLS_MERGE.out.bed, SORT_PEAK.out.sorted )
+}

tests/modules/CCBR/bedops/bedmap/nextflow.config

@@ -0,0 +1,7 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
+
+includeConfig '../../../../config/test_data_CCBR.config'

tests/modules/CCBR/bedops/bedmap/test.yml

@@ -0,0 +1,12 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml /bedmap
+- name: "bedops bedmap"
+  command: nextflow run ./tests/modules/CCBR/bedops/bedmap -entry test_bedops_bedmap -c ./tests/config/nextflow.config
+  tags:
+    - "bedops"
+    - "bedops/bedmap"
+  files:
+    - path: "output/bedops/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: "output/bedops/versions.yml"
+      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b