fix liniting

nf-core · Jan 24, 2025 · 76f9216 · 76f9216
1 parent e02d36c
commit 76f9216
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Showing 2 changed files with 13 additions and 9 deletions.
diff --git a/modules/nf-core/parabricks/deepvariant/main.nf b/modules/nf-core/parabricks/deepvariant/main.nf
@@ -7,8 +7,8 @@ process PARABRICKS_DEEPVARIANT {
     container "nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1"
 
     input:
-    tuple val(meta), path(bam), path(bai), path(interval_bed)
-    tuple val(meta1), path(fasta)
+    tuple val(meta), path(bam), path(bai), path(interval_file)
+    tuple val(ref_meta), path(fasta)
     path model_file
 
     output:
@@ -23,7 +23,7 @@ process PARABRICKS_DEEPVARIANT {
     def args = task.ext.args ?: ''
     def prefix     = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def output_file = ("--gvcf" =~ task.ext.args)? "${prefix}.g.vcf" : "${prefix}.vcf"
-    def interval_bed_option = interval_bed ? interval_bed.collect{"--interval-file $it"}.join(' ') : ""
+    def interval_file_option = interval_file ? interval_file.collect{"--interval-file $it"}.join(' ') : ""
     def model_command = model_file ? "--pb-model-file $model_file" : ""
     def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
 
@@ -33,7 +33,7 @@ process PARABRICKS_DEEPVARIANT {
         --ref $fasta \\
         --in-bam $bam \\
         --out-variants $output_file \\
-        ${interval_bed_option} \\
+        ${interval_file_option} \\
         ${num_gpus} \\
         ${model_command} \\
         $args

diff --git a/modules/nf-core/parabricks/deepvariant/meta.yml b/modules/nf-core/parabricks/deepvariant/meta.yml
@@ -21,11 +21,11 @@ input:
         description: |
           Groovy Map containing tumor sample information - id must match read groups for this sample.
           [ id:'test']
-    - input:
+    - bam:
         type: file
         description: bam file for sample to be variant called.
         pattern: "*.bam"
-    - input_index:
+    - bai:
         type: file
         description: bai index corresponding to input bam file. Only necessary if intervals
           are provided.
@@ -44,6 +44,10 @@ input:
         type: file
         description: reference fasta - must be unzipped.
         pattern: "*.fasta"
+  - - model_file:
+        type: file
+        description: custom deepvariant model file
+        pattern: "*,model"
 output:
   - vcf:
       - meta:
@@ -56,15 +60,15 @@ output:
           description: vcf file created with deepvariant (does not support .gz for normal vcf), optional
           pattern: "*.vcf"
   - gvcf:
-      - meta:          
+      - meta:
           type: map
           description: |
             Groovy Map containing sample information.
             e.g. [ id:'test' ]
-      - "*.g.vcf.gz":
+      - "*.g.vcf":
           type: file
           description: bgzipped gvcf created with deepvariant, optional
-          pattern: "*.g.vcf.gz"
+          pattern: "*.g.vcf"
   - versions:
       - versions.yml:
           type: file