Fixed slop file

software/bedtools/slop/main.nf

@@ -15,34 +15,29 @@ process BEDTOOLS_SLOP {
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
     } else {
-        container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
+        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
     }
 
 
     input:
-        tuple val(meta), path(beds), path (sizes)
+    tuple val(meta), path(beds), path (sizes)
 
     output:
-        tuple val(meta), path("*.slop.bed"), emit: bed
-        path  "*.version.txt", emit: version
+    tuple val(meta), path("*.slop.bed"), emit: bed
+    path  "*.version.txt", emit: version
 
     script:
-        def software = getSoftwareName(task.process)
-        def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-        def header = params.header ? "-header":''
-        def pct = params.pct ? "-pct":''
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    bedtools \\
+        slop \\
+        -i $beds \\
+        -g $sizes \\
+        $options.args \\
+        > ${prefix}.slop.bed
 
-        def symmetry = ''
-        if (meta.symmetry) {
+    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    """
 
-        """
-        slopBed -i $beds -g $sizes -b $params.b $header $pct $options.args> ${prefix}.slop.bed
-        bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
-        """
-        } else {
-        """
-        slopBed -i $beds -g $sizes -l $params.l -r $params.r $header $pct $options.args> ${prefix}.slop.bed
-        bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
-        """
-        }
 }

tests/software/bedtools/main.nf

@@ -6,8 +6,7 @@ include { BEDTOOLS_COMPLEMENT } from '../../../software/bedtools/complement/main
 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_SLOP} from '../../../software/bedtools/slop/main.nf' addParams( options: [args: '-l 15 -r 30'] )
 include { BEDTOOLS_SORT } from '../../../software/bedtools/sort/main.nf' addParams( options: [:] )
 
 
@@ -47,28 +46,12 @@ workflow test_bedtools_merge {
     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 {
+workflow test_bedtools_slop {
     def input = []
-    input = [ [ id:'test', symmetry: false],
+    input = [ [ id:'test'],
               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 )
+    BEDTOOLS_SLOP ( input )
 }
 
 workflow test_bedtools_sort {

tests/software/bedtools/test.yml

@@ -46,7 +46,7 @@
       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
+  command: nextflow run ./tests/software/bedtools/ -profile docker -entry test_bedtools_slop -c tests/config/nextflow.config
   tags:
     - bedtools
     - bedtools_slop
@@ -54,11 +54,3 @@
     - 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