diff --git a/CHANGELOG.md b/CHANGELOG.md
index c814b8ac..f5fd84c8 100644
--- a/CHANGELOG.md
+++ b/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.
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 7fb907c9..297ebfd6 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
report_comment: >
- This report has been generated by the nf-core/atacseq
+ This report has been generated by the nf-core/atacseq
analysis pipeline. For information about how to interpret these results, please see the
- documentation.
+ documentation.
data_format: "yaml"
diff --git a/lib/WorkflowAtacseq.groovy b/lib/WorkflowAtacseq.groovy
index 235ec444..663df1fb 100755
--- 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/modules.json b/modules.json
index b95992e1..962c8dc3 100644
--- a/modules.json
+++ b/modules.json
@@ -92,7 +92,7 @@
},
"homer/annotatepeaks": {
"branch": "master",
- "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+ "git_sha": "ffc27c68870f5f67e541bb67d94e03c597f75257",
"installed_by": ["modules"]
},
"khmer/uniquekmers": {
diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf
index cfc140f5..b6a4c6bd 100644
--- a/modules/nf-core/homer/annotatepeaks/main.nf
+++ b/modules/nf-core/homer/annotatepeaks/main.nf
@@ -15,6 +15,7 @@ process HOMER_ANNOTATEPEAKS {
output:
tuple val(meta), path("*annotatePeaks.txt"), emit: txt
+ tuple val(meta), path("*annStats.txt"), emit: stats, optional: true
path "versions.yml" , emit: versions
when:
diff --git a/modules/nf-core/homer/annotatepeaks/meta.yml b/modules/nf-core/homer/annotatepeaks/meta.yml
index b815e975..2c6e52a1 100644
--- a/modules/nf-core/homer/annotatepeaks/meta.yml
+++ b/modules/nf-core/homer/annotatepeaks/meta.yml
@@ -39,6 +39,10 @@ output:
type: file
description: The annotated peaks
pattern: "*annotatePeaks.txt"
+ - annotation_stats:
+ type: file
+ description: the annStats file output from -annStats parameter
+ pattern: "*annStats.txt"
- versions:
type: file
description: File containing software versions
diff --git a/nextflow.config b/nextflow.config
index 6cdb5ae2..1d39f5c9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -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'
}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index fd39fea4..2e384c9e 100644
--- 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",