Remove unnecessary (and sometimes problematic) input channel

nf-core · Jul 27, 2023 · d591036 · d591036
1 parent 286545e
commit d591036
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 7 deletions.
diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf
@@ -12,7 +12,6 @@ process CENTRIFUGE_CENTRIFUGE {
     path db
     val save_unaligned
     val save_aligned
-    val sam_format
 
     output:
     tuple val(meta), path('*report.txt')                 , emit: report
@@ -38,7 +37,6 @@ process CENTRIFUGE_CENTRIFUGE {
         unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
     }
-    def sam_output = sam_format ? "--out-fmt 'sam'" : ''
     """
     ## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
     db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/\\.1.cf\$//'`
@@ -51,7 +49,6 @@ process CENTRIFUGE_CENTRIFUGE {
         $unaligned \\
         $aligned \\
         $sam_output \\
-        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/tests/modules/nf-core/centrifuge/centrifuge/main.nf b/tests/modules/nf-core/centrifuge/centrifuge/main.nf
@@ -12,10 +12,9 @@ workflow test_centrifuge_centrifuge_single_end {
     db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
     save_unaligned = true
     save_aligned = false
-    sam_format = false
 
     UNTAR ( db )
-    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
+    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned )
 
 }
 
@@ -27,10 +26,9 @@ workflow test_centrifuge_centrifuge_paired_end {
      db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
      save_unaligned = true
      save_aligned = false
-     sam_format = false
 
     UNTAR ( db )
-    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
+    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned )
 
 
 }