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",