removed flag

UPHL-BioNGS · Jun 26, 2024 · 6f90843 · 6f90843
1 parent d46878d
commit 6f90843
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git a/modules/local/pbptyper.nf b/modules/local/pbptyper.nf
@@ -8,7 +8,7 @@ process pbptyper {
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
-  tuple val(meta), file(contigs), val(flag)
+  tuple val(meta), file(contigs)
 
   output:
   path "pbptyper/${meta.id}.tsv"   , emit: collect
@@ -17,7 +17,7 @@ process pbptyper {
   path "versions.yml"              , emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args   = task.ext.args   ?: ''

diff --git a/modules/local/seqsero2.nf b/modules/local/seqsero2.nf
@@ -7,7 +7,7 @@ process seqsero2 {
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
-  tuple val(meta), file(file), val(flag)
+  tuple val(meta), file(file)
 
   output:
   path "seqsero2/*/*"                                    , emit: files
@@ -16,7 +16,7 @@ process seqsero2 {
   path  "versions.yml"                          , emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args = task.ext.args     ?: '-m a -b mem'

diff --git a/modules/local/serotypefinder.nf b/modules/local/serotypefinder.nf
@@ -8,7 +8,7 @@ process serotypefinder {
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}  
 
   input:
-  tuple val(meta), file(file), val(flag), file(script)
+  tuple val(meta), file(file), file(script)
 
   output:
   path "serotypefinder/*/*"                 , emit: files
@@ -17,7 +17,7 @@ process serotypefinder {
   path "versions.yml"                       , emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args   = task.ext.args   ?: ''

diff --git a/modules/local/shigatyper.nf b/modules/local/shigatyper.nf
@@ -8,7 +8,7 @@ process shigatyper {
   time          '10m'
 
   input:
-  tuple val(meta), file(input), val(flag), file(script)
+  tuple val(meta), file(input), file(script)
 
   output:
   path "shigatyper/*_shigatyper.tsv", optional: true, emit: files
@@ -17,7 +17,7 @@ process shigatyper {
   path "versions.yml", emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args = task.ext.args ?: ''