add decompress possibilities to bgzip (#1540)

* add decompress possibilities to bgzip

* spacing

modules/tabix/bgzip/main.nf

@@ -11,17 +11,20 @@ process TABIX_BGZIP {
     tuple val(meta), path(input)
 
     output:
-    tuple val(meta), path("*.gz"), emit: gz
+    tuple val(meta), path("${prefix}*"), emit: output
-    path  "versions.yml"         , emit: versions
+    path  "versions.yml"               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    in_bgzip = input.toString().endsWith(".gz")
+    command1 = in_bgzip ? '-d' : '-c'
+    command2 = in_bgzip ? ''   : " > ${prefix}.${input.getExtension()}.gz"
     """
-    bgzip -c $args $input > ${prefix}.${input.getExtension()}.gz
+    bgzip $command1 $args -@${task.cpus} $input $command2
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/tabix/bgzip/meta.yml

@@ -1,13 +1,14 @@
 name: tabix_bgzip
-description: Compresses files
+description: Compresses/decompresses files
 keywords:
   - compress
+  - decompress
   - bgzip
   - tabix
 tools:
   - bgzip:
       description: |
-        Bgzip compresses files in a similar manner to, and compatible with, gzip.
+        Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.
       homepage: https://www.htslib.org/doc/tabix.html
       documentation: http://www.htslib.org/doc/bgzip.html
       doi: 10.1093/bioinformatics/btp352
@@ -18,19 +19,19 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - file:
+  - input:
       type: file
-      description: text file
+      description: file to compress or to decompress
 output:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - file:
+  - output:
       type: file
-      description: Output compressed file
+      description: Output compressed/decompressed file
-      pattern: "*.{gz}"
+      pattern: "*."
   - versions:
       type: file
       description: File containing software versions

tests/config/test_data.config

@@ -397,7 +397,7 @@ params {
                 hello = "${test_data_dir}/generic/txt/hello.txt"
             }
             'cnn' {
-                 reference = "${test_data_dir}/generic/cnn/reference.cnn"
+                reference = "${test_data_dir}/generic/cnn/reference.cnn"
             }
             'cooler'{
                 test_pairix_pair_gz                           = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"

tests/modules/tabix/bgzip/main.nf

@@ -4,10 +4,18 @@ nextflow.enable.dsl = 2
 
 include { TABIX_BGZIP } from '../../../../modules/tabix/bgzip/main.nf'
 
-workflow test_tabix_bgzip {
+workflow test_tabix_bgzip_compress {
     input = [ [ id:'test' ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
             ]
 
     TABIX_BGZIP ( input )
 }
+
+workflow test_tabix_bgzip_decompress {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ]
+            ]
+
+    TABIX_BGZIP ( input )
+}

tests/modules/tabix/bgzip/test.yml

@@ -1,8 +1,16 @@
-- name: tabix bgzip
+- name: tabix bgzip compress
-  command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config
+  command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip_compress -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config
   tags:
     - tabix
     - tabix/bgzip
   files:
     - path: ./output/tabix/test.vcf.gz
       md5sum: fc178eb342a91dc0d1d568601ad8f8e2
+- name: tabix bgzip decompress
+  command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip_decompress -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config
+  tags:
+    - tabix
+    - tabix/bgzip
+  files:
+    - path: ./output/tabix/test.bed
+      md5sum: fe4053cf4de3aebbdfc3be2efb125a74