bedToBigBed AutoSql option (#1981)

* Added missing "ucsc" tags (as per the convention)

* Added support for the -as input file

* Added a test

modules/ucsc/bedtobigbed/main.nf

@@ -11,6 +11,7 @@ process UCSC_BEDTOBIGBED {
     input:
     tuple val(meta), path(bed)
     path  sizes
+    path  autosql
 
     output:
     tuple val(meta), path("*.bigBed"), emit: bigbed
@@ -22,11 +23,13 @@ process UCSC_BEDTOBIGBED {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def as_option = autosql ? "-as=${autosql}" : ""
     def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     bedToBigBed \\
         $bed \\
         $sizes \\
+        $as_option \\
         $args \\
         ${prefix}.bigBed
 

modules/ucsc/bedtobigbed/meta.yml

@@ -26,6 +26,10 @@ input:
       type: file
       description: chromosome sizes file
       pattern: "*.{sizes}"
+  - autosql:
+      type: file
+      description: autoSql file to describe the columns of the BED file
+      pattern: "*.{as}"
 
 output:
   - meta:

tests/config/test_data.config

@@ -23,6 +23,7 @@ params {
                 test2_bed                                      = "${test_data_dir}/genomics/sarscov2/genome/bed/test2.bed"
                 test_bed12                                     = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed12"
                 baits_bed                                      = "${test_data_dir}/genomics/sarscov2/genome/bed/baits.bed"
+                bed_autosql                                    = "${test_data_dir}/genomics/sarscov2/genome/bed/bed6alt.as"
 
                 reference_cnn                                  = "${test_data_dir}/genomics/sarscov2/genome/cnn/reference.cnn"
 

tests/modules/ucsc/bedgraphtobigwig/test.yml

@@ -1,6 +1,7 @@
 - name: ucsc bedgraphtobigwig
   command: nextflow run ./tests/modules/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedgraphtobigwig/nextflow.config
   tags:
+    - ucsc
     - ucsc/bedgraphtobigwig
   files:
     - path: output/ucsc/test.bigWig

tests/modules/ucsc/bedtobigbed/main.nf

@@ -3,12 +3,23 @@
 nextflow.enable.dsl = 2
 
 include { UCSC_BEDTOBIGBED } from '../../../../modules/ucsc/bedtobigbed/main.nf'
+include { UCSC_BEDTOBIGBED as UCSC_BEDTOBIGBED_AS } from '../../../../modules/ucsc/bedtobigbed/main.nf'
 
 workflow test_ucsc_bedtobigbed {
     input = [ [ id: 'test' ], // meta map 
-              [ file(params.test_data['sarscov2']['genome']['test_bed12'], checkIfExists: true ) ] 
+              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ]
             ]
     sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
 
-    UCSC_BEDTOBIGBED ( input, sizes )
+    UCSC_BEDTOBIGBED ( input, sizes, [] )
+}
+
+workflow test_ucsc_bedtobigbed_autosql {
+    input = [ [ id: 'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ]
+            ]
+    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+    autosql = file(params.test_data['sarscov2']['genome']['bed_autosql'], checkIfExists: true)
+
+    UCSC_BEDTOBIGBED_AS ( input, sizes, autosql )
 }

tests/modules/ucsc/bedtobigbed/nextflow.config

@@ -2,4 +2,7 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    withName: UCSC_BEDTOBIGBED_AS {
+        ext.args = "-type=bed3+3"
+    }
 }

tests/modules/ucsc/bedtobigbed/test.yml

@@ -1,7 +1,16 @@
 - 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
     - ucsc/bedtobigbed
   files:
     - path: output/ucsc/test.bigBed
-      md5sum: 98cf0d0baa3ae5a330c80afbb8bc2b18
+      md5sum: 3c2400aab8f7a3ac333905c7484d9a24
+- name: ucsc bedtobigbed autosql
+  command: nextflow run ./tests/modules/ucsc/bedtobigbed -entry test_ucsc_bedtobigbed_autosql -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedtobigbed/nextflow.config
+  tags:
+    - ucsc
+    - ucsc/bedtobigbed
+  files:
+    - path: output/ucsc/test.bigBed
+      md5sum: 6dc69a14b95bcceee98e9e6b3c3def09