Apply linting

nf-core · May 30, 2024 · f1a365f · f1a365f
1 parent 3cd29a9
commit f1a365f
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Showing 3 changed files with 6 additions and 2 deletions.
diff --git a/modules/local/markdups/Dockerfile b/modules/local/markdups/Dockerfile
@@ -21,7 +21,7 @@ RUN \
     conda clean -yaf
 
 RUN \
-  wget -P /tmp/ https://github.com/hartwigmedical/hmftools/releases/download/mark-dups-v1.1.6_beta/mark-dups_v1.1.6_beta.jar
+    wget -P /tmp/ https://github.com/hartwigmedical/hmftools/releases/download/mark-dups-v1.1.6_beta/mark-dups_v1.1.6_beta.jar
 
 # Move Conda environment into standard BioContainers base image
 FROM quay.io/bioconda/base-glibc-busybox-bash:2.1.0

diff --git a/nextflow.config b/nextflow.config
@@ -15,6 +15,10 @@ params {
     // Workflow mode
     mode = null
 
+    // Force options
+    force_genome = false
+    force_panel  = false
+
     // Read processing and alignment options
     max_fastq_records = 10000000
     umi_length        = 0
@@ -27,7 +31,6 @@ params {
 
     // Reference genome information; iGenomes is effectively disabled but retained for linting
     genome          = null
-    force_genome    = false
     igenomes_base   = 's3://ngi-igenomes/igenomes'
     igenomes_ignore = true
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -63,6 +63,7 @@
                 "force_panel": {
                     "type": "boolean",
                     "description": "Skip check for known panels.",
+                    "default": false,
                     "fa_icon": "fas fa-palette"
                 },
                 "processes_manual": {