Added support for task.ext.args (#1954)

* Added support for `task.ext.args`

* Renamed the module since it can now process any sort of BED file

modules/ucsc/bedtobigbed/main.nf

@@ -1,4 +1,4 @@
-process UCSC_BED12TOBIGBED {
+process UCSC_BEDTOBIGBED {
     tag "$meta.id"
     label 'process_medium'
 
@@ -27,6 +27,7 @@ process UCSC_BED12TOBIGBED {
     bedToBigBed \\
         $bed \\
         $sizes \\
+        $args \\
         ${prefix}.bigBed
 
     cat <<-END_VERSIONS > versions.yml

modules/ucsc/bedtobigbed/meta.yml

@@ -1,11 +1,11 @@
-name: ucsc_bed12tobigbed
-description: Convert file from bed12 to bigBed format
+name: ucsc_bedtobigbed
+description: Convert file from bed to bigBed format
 keywords:
-  - bed12
+  - bed
   - bigbed
 tools:
   - ucsc:
-      description: Convert file from bed12 to bigBed format
+      description: Convert file from bed to bigBed format
       homepage: None
       documentation: None
       tool_dev_url: None
@@ -20,8 +20,8 @@ input:
         e.g. [ id:'test', single_end:false ]
   - bed:
       type: file
-      description: bed12 file
-      pattern: "*.{bed,bed12}"
+      description: bed file
+      pattern: "*.{bed}"
   - sizes:
       type: file
       description: chromosome sizes file

tests/config/pytest_modules.yml

@@ -2219,9 +2219,9 @@ trimmomatic:
   - modules/trimmomatic/**
   - tests/modules/trimmomatic/**
 
-ucsc/bed12tobigbed:
-  - modules/ucsc/bed12tobigbed/**
-  - tests/modules/ucsc/bed12tobigbed/**
+ucsc/bedtobigbed:
+  - modules/ucsc/bedtobigbed/**
+  - tests/modules/ucsc/bedtobigbed/**
 
 ucsc/bedclip:
   - modules/ucsc/bedclip/**

tests/modules/ucsc/bed12tobigbed/test.yml

@@ -1,7 +0,0 @@
-- name: ucsc bed12tobigbed
-  command: nextflow run ./tests/modules/ucsc/bed12tobigbed -entry test_ucsc_bed12tobigbed -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bed12tobigbed/nextflow.config
-  tags:
-    - ucsc/bed12tobigbed
-  files:
-    - path: output/ucsc/test.bigBed
-      md5sum: 98cf0d0baa3ae5a330c80afbb8bc2b18

tests/modules/ucsc/bedtobigbed/main.nf

@@ -2,13 +2,13 @@
 
 nextflow.enable.dsl = 2
 
-include { UCSC_BED12TOBIGBED } from '../../../../modules/ucsc/bed12tobigbed/main.nf'
+include { UCSC_BEDTOBIGBED } from '../../../../modules/ucsc/bedtobigbed/main.nf'
 
-workflow test_ucsc_bed12tobigbed {
+workflow test_ucsc_bedtobigbed {
     input = [ [ id: 'test' ], // meta map 
               [ file(params.test_data['sarscov2']['genome']['test_bed12'], checkIfExists: true ) ] 
             ]
     sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
 
-    UCSC_BED12TOBIGBED ( input, sizes )
+    UCSC_BEDTOBIGBED ( input, sizes )
 }

tests/modules/ucsc/bedtobigbed/test.yml

@@ -0,0 +1,7 @@
+- name: ucsc bedtobigbed
+  command: nextflow run ./tests/modules/ucsc/bedtobigbed -entry test_ucsc_bedtobigbed -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedtobigbed/nextflow.config
+  tags:
+    - ucsc/bedtobigbed
+  files:
+    - path: output/ucsc/test.bigBed
+      md5sum: 98cf0d0baa3ae5a330c80afbb8bc2b18