Removed extraneous modules and updated removegenes module

software/bedtools/fixbedcoordinates/functions.nf

@@ -1,59 +0,0 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
-
-/*
- * Extract name of software tool from process name using $task.process
- */
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
-    return options
-}
-
-/*
- * Tidy up and join elements of a list to return a path string
- */
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-/*
- * Function to save/publish module results
- */
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}

software/bedtools/fixbedcoordinates/main.nf

@@ -1,41 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-def VERSION = '2.29'
-
-process BEDTOOLS_FIXBEDCOORDINATES {
-    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) }
-
-    conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
-    if (workflow.containerEngine == 'singularity' && !params.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("*.sloprefseq.bed")
-
-    output:
-        tuple val(meta), path("*.sloprefseqsorted.bed"), emit: bed
-        path  "*.version.txt", emit: version
-
-    script:
-        def software = getSoftwareName(task.process)
-        def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-        // sorted via chromosome, then by start position
-        """
-         awk -F '\\t' 'length($1) <= 5 {{ print }}' ${prefix}.sloprefseq.bed |
-         awk '{{ if ($2 > $3) {{ t = $2; $2 = $3; $3 = t; }} \
-         else if ($2 == $3) {{ $3 += 1; }} print $0; }}' OFS='\\t' - \
-         | sort-bed > ${prefix}.sloprefseqsorted.bed
-         echo $VERSION > ${software}.version.txt
-        """
-}

software/bedtools/fixbedcoordinates/meta.yml

@@ -1,55 +0,0 @@
-name: bedtools_fixbedcoordinates
-description: Removes chrXYZ_random entries in hg18, fixes alignments if start is after the end and
-sorts the entries
-
-keywords:
-    - bed
-    - length
-    - sort
-
-    tools:
-    - bedtools:
-        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/
-
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-input:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - bed:
-        type: file
-        description: List of bed files
-        pattern: "*.{bed}"
-output:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - bed:
-        type: file
-        description: Edited bed file
-        pattern: "*.{bed}"
-    - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"

software/bedtools/removegenes/main.nf

@@ -4,9 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 def options    = initOptions(params.options)
 
-def VERSION = '4.11'
-
-process BEDTOOLS_SLOPEREFSEQ {
+process BEDTOOLS_REMOVEGENES {
     tag "$meta.id"
     label 'process_medium'
     publishDir "${params.outdir}",
@@ -21,11 +19,11 @@ process BEDTOOLS_SLOPEREFSEQ {
     }
 
     input:
-        path metatranscripts
-        tuple val(meta), path("*.sloprefseqsorted.bed")
+        tuple val(meta), path(slopbed)
+        path metatranscript
 
     output:
-        tuple val(meta), path("*.nogenes.bed"), emit: bed
+        tuple val(meta), path("*.nogenes.bed"), emit: nogenesbed
         path  "*.version.txt", emit: version
 
     script:
@@ -33,8 +31,8 @@ process BEDTOOLS_SLOPEREFSEQ {
         def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
         // sorted via chromosome, then by start position
         """
-        bedtools intersect -a $metatranscripts -b ${prefix}.sloprefseqsorted.bed -v \\
-        sort -k1,1 -k2,2n > {prefix}.nogenes.bed 
-        echo $VERSION > ${software}.version.txt
+        bedtools intersect -a $metatranscript -b $slopbed -v \\
+        | sortBed > ${prefix}.nogenes.bed 
+        bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
         """
 }

software/bedtools/removegenes/meta.yml

@@ -1,5 +1,5 @@
 name: bedtools_removegenes
-description: Adds 1 KB to the front of the genes and 10 KB to the end of the sequence.
+description: Removes the intergenic regions from GRO-Seq Transcripts
 
 
 keywords:

software/bedtools/slopRefseq/main.nf

@@ -1,39 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-def VERSION = '4.11'
-
-process BEDTOOLS_SLOPEREFSEQ {
-    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) }
-
-    conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
-    if (workflow.containerEngine == 'singularity' && !params.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:
-        path sizes
-        tuple val(meta), path(beds)
-
-    output:
-        tuple val(meta), path("*.sloprefseq.bed"), emit: bed
-        path  "*.version.txt", emit: version
-
-    script:
-        def software = getSoftwareName(task.process)
-        def beds_files = beds.sort()
-        def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-        """
-        slopBed -i $beds -g $sizes -l ${params.upstream} -r {params.downstream} > ${prefix}.sloprefseq.bed
-        echo $VERSION > ${software}.version.txt
-        """
-}

software/bedtools/slopRefseq/meta.yml

@@ -1,55 +0,0 @@
-name: bedtools_sloperefseq
-description: Adds 1 KB to the front of the genes and 10 KB to the end of the sequence.
-
-
-keywords:
-    - bed
-    - slopBed
-    - downstream
-    - upstream
-tools:
-    - bedtools:
-        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/
-
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-input:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - bed:
-        type: file
-        description: List of bed files
-        pattern: "*.{bed}"
-output:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - bed:
-        type: file
-        description: Edited bed file
-        pattern: "*.{bed}"
-    - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"

software/bedtools/sloprefseq/functions.nf

@@ -1,59 +0,0 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
-
-/*
- * Extract name of software tool from process name using $task.process
- */
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
-    return options
-}
-
-/*
- * Tidy up and join elements of a list to return a path string
- */
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-/*
- * Function to save/publish module results
- */
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}

software/bedtools/sloprefseq/main.nf

@@ -1,39 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [upstream: 1,
-                  downstream: 10 ]
-
-def options    = initOptions(params.options)
-
-process BEDTOOLS_SLOPREFSEQ {
-    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) }
-
-    conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
-    if (workflow.containerEngine == 'singularity' && !params.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  sizes
-
-    output:
-        tuple val(meta), path("*.sloprefseq.bed"), emit: bed
-        path  "*.version.txt", emit: version
-
-    script:
-        def software = getSoftwareName(task.process)
-        def beds_files = beds.sort()
-        def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-        """
-        slopBed -i ln -s ${beds[0]} -g ln -s $sizes -l ${params.upstream} -r ${params.downstream} > ${prefix}.sloprefseq.bed
-        bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
-        """
-}

software/bedtools/sloprefseq/meta.yml

@@ -1,55 +0,0 @@
-name: bedtools_sloperefseq
-description: Adds 1 KB to the front of the genes and 10 KB to the end of the sequence.
-
-
-keywords:
-    - bed
-    - slopBed
-    - downstream
-    - upstream
-tools:
-    - bedtools:
-        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/
-
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-input:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - bed:
-        type: file
-        description: List of bed files
-        pattern: "*.{bed}"
-output:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - bed:
-        type: file
-        description: Edited bed file
-        pattern: "*.{bed}"
-    - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"

software/bedtools/sloprefseq/test/input/A.bed

@@ -1,5 +0,0 @@
-chr1	951	1061
-chr1	1300	1420
-chr1	1400	1500
-
-

software/bedtools/sloprefseq/test/input/genome.sizes

@@ -1 +0,0 @@
-chr1	1780869

software/bedtools/sloprefseq/test/main.nf

@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.preview.dsl = 2
-
-include { BEDTOOLS_SLOPREFSEQ } from '../../sloprefseq/main.nf' addParams( options: [publish_dir:'test_bed_file'])
-
-// Define input channels
-
-// Run the workflow
-workflow test_bed_file{
-    def input = []
-    input = [ [ id:'test', single_end:true ], 
-              [ file("${baseDir}/input/A.bed", checkIfExists: true),] ]
-
-    BEDTOOLS_SLOPREFSEQ (
-        input, 
-        file("${baseDir}/input/genome.sizes", checkIfExists: true)
-    )
-    
-
-}
-
-workflow {
-    test_bed_file()
-}

software/bedtools/sloprefseq/test/nextflow.config

@@ -1,20 +0,0 @@
-  
-params {
-    outdir = "output/"
-    publish_dir_mode = "copy"
-    enable_conda = false
-}
-
-profiles {
-    conda  {
-        params.enable_conda = true
-    }
-    docker {
-        docker.enabled = true
-        docker.runOptions = '-u \$(id -u):\$(id -g)'
-    }
-    singularity {
-        singularity.enabled = true
-        singularity.autoMounts = true
-    }
-}