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Co-authored-by: James A. Fellows Yates <[email protected]>
nf-core · Jul 28, 2023 · 526ce85 · 526ce85
1 parent 0ede14b
commit 526ce85
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Showing 3 changed files with 3 additions and 5 deletions.
diff --git a/modules/nf-core/topas/gencons/main.nf b/modules/nf-core/topas/gencons/main.nf
@@ -25,7 +25,6 @@ process TOPAS_GENCONS {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
-
     """
 
     topas \\

diff --git a/modules/nf-core/topas/gencons/meta.yml b/modules/nf-core/topas/gencons/meta.yml
@@ -13,7 +13,6 @@ tools:
       doi: "10.1038/s41598-017-17723-1"
       licence: "['CC-BY']"
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
   - meta:
       type: map
@@ -45,7 +44,7 @@ output:
 
   - fasta:
       type: file
-      description: Gzip consensus fasta file
+      description: Gzipped consensus fasta file with bases under threshold replaced with Ns
       pattern: "*.fasta.gz"
 
   - ccf:

diff --git a/tests/modules/nf-core/topas/gencons/main.nf b/tests/modules/nf-core/topas/gencons/main.nf
@@ -3,11 +3,11 @@
 nextflow.enable.dsl = 2
 
 include { GATK_UNIFIEDGENOTYPER } from '../../../../modules/nf-core/gatk/unifiedgenotyper/main.nf'
-include { TOPAS_GENCONS } from '../../../../../modules/nf-core/topas/gencons/main.nf'
+include { TOPAS_GENCONS         } from '../../../../../modules/nf-core/topas/gencons/main.nf'
 
 workflow test_topas_gencons {
 
-    input_gatk     = [ [ id:'test' ], // meta map
+    input_gatk = [ [ id:'test' ], // meta map
                   file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
                   file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
                 ]