Merge pull request #324 from nf-core/dev

Dev -> Master for 2.1.2 release

Author: JoseEspinosa

CHANGELOG.md

@@ -3,6 +3,13 @@
 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).
 
+## [[2.1.2](https://github.com/nf-core/atacseq/releases/tag/2.1.2)] - 2022-08-07
+
+### Enhancements & fixes
+
+- [[#322](https://github.com/nf-core/atacseq/issues/322)]Remove fasta from required schema parameters so that when launching from tools it is not required.
+- Updates `homer_annotatepeaks` module.
+
 ## [[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.

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/atacseq/2.1.1" target="_blank">nf-core/atacseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/atacseq/2.1.2" target="_blank">nf-core/atacseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/atacseq/2.1.1/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/atacseq/2.1.2/output" target="_blank">documentation</a>.
 
 data_format: "yaml"
 

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)

modules.json

@@ -92,7 +92,7 @@
                     },
                     "homer/annotatepeaks": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "ffc27c68870f5f67e541bb67d94e03c597f75257",
                         "installed_by": ["modules"]
                     },
                     "khmer/uniquekmers": {

modules/nf-core/homer/annotatepeaks/main.nf

@@ -286,7 +286,7 @@ manifest {
     description     = """ATACSeq peak-calling and differential analysis pipeline."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.1.1'
+    version         = '2.1.2'
     doi             = 'https://doi.org/10.5281/zenodo.2634132'
 }
 

modules/nf-core/homer/annotatepeaks/meta.yml

@@ -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",