Fix linting

Author: sainsachiko

modules/nf-core/pbmarkdup/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pbmarkdup==1.2.0
+  - bioconda::pbmarkdup=1.2.0

modules/nf-core/pbmarkdup/main.nf

@@ -11,17 +11,17 @@ process PBMARKDUP {
     tuple val(meta), path(input)
 
     output:
-    tuple val(meta), path("*.{bam,f*a,/.*f.*\\.gz/}") , emit: markduped
-    path "versions.yml"                               , emit: versions
+    tuple val(meta), path("${prefix}.${suffix}"), emit: markduped
+    path "versions.yml"                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args  = task.ext.args  ?: ''
 
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = input.getExtension()
+    prefix = task.ext.prefix ?: "${meta.id}"
+    suffix = input.getExtension()
 
     """
     pbmarkdup \\
@@ -37,8 +37,8 @@ process PBMARKDUP {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = input.getExtension()
+    prefix = task.ext.prefix ?: "${meta.id}"
+    suffix = input.getExtension()
     """
     touch ${prefix}.${suffix}
 

modules/nf-core/pbmarkdup/meta.yml

@@ -1,7 +1,7 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "pbmarkdup"
 description: |
-  Takes one or multiple sequencing chips of an amplified library as HiFi reads and marks or removes 
+  Takes one or multiple sequencing chips of an amplified library as HiFi reads and marks or removes
   duplicates.
 keywords:
   - markdup
@@ -11,9 +11,9 @@ keywords:
 tools:
   - pbmarkdup:
       description: |
-        pbmarkdup identifies and marks duplicate reads in PacBio HiFi (CCS) data. It clusters 
-        highly similar CCS reads to detect PCR duplicates and flags them in the BAM output 
-        (duplicate bit 0x400), optionally removing duplicates. 
+        pbmarkdup identifies and marks duplicate reads in PacBio HiFi (CCS) data. It clusters
+        highly similar CCS reads to detect PCR duplicates and flags them in the BAM output
+        (duplicate bit 0x400), optionally removing duplicates.
       homepage: https://github.com/PacificBiosciences/pbmarkdup
       documentation: https://github.com/PacificBiosciences/pbmarkdup
       licence: ["BSD-3-Clause"]
@@ -31,20 +31,24 @@ input:
         pattern: "*.{bam,f*a,/.*f.*\\.gz/}"
         ontologies:
           - edam: http://edamontology.org/format_2546 # FASTA-like
+          - edam: "http://edamontology.org/format_1930" # FASTQ
+          - edam: "http://edamontology.org/format_2572" # BAM
 output:
   markduped:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
-      - "*.${suffix}":
+      - ${prefix}.${suffix}:
           type: file
           description: |
             Markduplicated sequencing reads in the same format as the input file.
           pattern: "*.{bam,f*a,/.*f.*\\.gz/}"
           ontologies:
-            - edam: http://edamontology.org/format_3003
+            - edam: http://edamontology.org/format_2546 # FASTA-like
+            - edam: "http://edamontology.org/format_1930" # FASTQ
+            - edam: "http://edamontology.org/format_2572" # BAM
   versions:
     - versions.yml:
         type: file
@@ -55,4 +59,4 @@ output:
 authors:
   - "@sainsachiko"
 maintainers:
-  - "@sainsachiko"
+  - "@sainsachiko"

modules/nf-core/pbmarkdup/tests/main.nf.test

@@ -6,7 +6,7 @@ nextflow_process {
     process "PBMARKDUP"
 
     tag "modules"
-    tag "modules_sangertol"
+    tag "modules_nfcore"
     tag "pbmarkdup"
 
     config './nextflow.config'