Check for fasta file via initialise instead of schema

nf-core · Jul 27, 2023 · 7a45b50 · 7a45b50
1 parent 6736e37
commit 7a45b50
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,10 +3,11 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 2.2.0dev - [date]
-
+## 2.1.2dev - [date]
 ### Enhancements & fixes
 
+- Remove fasta from required schema parameter so that when launching from tools it is not required.
+
 ## [[2.1.1](https://github.com/nf-core/atacseq/releases/tag/2.1.1)] - 2022-07-21
 
 - Minor patch release to fix AWS full test.

diff --git a/lib/WorkflowAtacseq.groovy b/lib/WorkflowAtacseq.groovy
@@ -13,6 +13,10 @@ class WorkflowAtacseq {
     public static void initialise(params, log) {
         genomeExistsError(params, log)
 
+        if (!params.fasta) {
+            Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
+        }
+
         if (!params.gtf && !params.gff) {
             log.error "No GTF or GFF3 annotation specified! The pipeline requires at least one of these files."
             System.exit(1)

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -207,8 +207,7 @@
                     "help_text": "By default takes the value of the mito_name parameter, if set. However, some plants and algae have chloroplast genomes in addition to a mitochondrial genome and thus mito_name can have values as multiple names that are separated by a | symbol that will break ataqv, in these cases this parameter can be used to overwrite these values.",
                     "fa_icon": "fas fa-signature"
                 }
-            },
-            "required": ["fasta"]
+            }
         },
         "adapter_trimming_options": {
             "title": "Adapter trimming options",