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Merge pull request #324 from nf-core/dev
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Dev -> Master for 2.1.2 release
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JoseEspinosa authored Aug 7, 2023
2 parents 415795d + df5b0e1 commit 1a1dbe5
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7 changes: 7 additions & 0 deletions CHANGELOG.md
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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.
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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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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"

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4 changes: 4 additions & 0 deletions lib/WorkflowAtacseq.groovy
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion modules.json
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},
"homer/annotatepeaks": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "ffc27c68870f5f67e541bb67d94e03c597f75257",
"installed_by": ["modules"]
},
"khmer/uniquekmers": {
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1 change: 1 addition & 0 deletions modules/nf-core/homer/annotatepeaks/main.nf

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4 changes: 4 additions & 0 deletions modules/nf-core/homer/annotatepeaks/meta.yml

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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -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'
}

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3 changes: 1 addition & 2 deletions nextflow_schema.json
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"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",
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