From 47e5b214f1e76e7eb12a1fdcc103b0237b0e52d1 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 24 Jul 2023 10:58:25 +0200 Subject: [PATCH 01/10] Bump pipeline version to 2.2.0dev --- CHANGELOG.md | 4 ++++ nextflow.config | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c814b8ac..804efb67 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,10 @@ 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] + +### Enhancements & fixes + ## [[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/nextflow.config b/nextflow.config index 6cdb5ae2..7fc83c34 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 = '2.2.0dev' doi = 'https://doi.org/10.5281/zenodo.2634132' } From 9611bf2314f5302c4f25df62b74cf9f9a5d17d1f Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 24 Jul 2023 11:08:50 +0200 Subject: [PATCH 02/10] Bump version also in multiqc_config --- assets/multiqc_config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 7fb907c9..f902256a 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" From 7a45b5064a183b2def342aa2c13c6d105a2d76fd Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Thu, 27 Jul 2023 23:43:56 +0200 Subject: [PATCH 03/10] Check for fasta file via initialise instead of schema --- CHANGELOG.md | 5 +++-- lib/WorkflowAtacseq.groovy | 4 ++++ nextflow_schema.json | 3 +-- 3 files changed, 8 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 804efb67..09c6c298 100644 --- 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 index 235ec444..b4dcae39 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/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", From 7d08a7e055c4b72505e7949aa31b0a09c40ad667 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Thu, 27 Jul 2023 23:57:16 +0200 Subject: [PATCH 04/10] Update hommer_annotatepeaks module --- modules.json | 2 +- modules/nf-core/homer/annotatepeaks/main.nf | 1 + modules/nf-core/homer/annotatepeaks/meta.yml | 4 ++++ 3 files changed, 6 insertions(+), 1 deletion(-) 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 From 092906ec508f724a985dfa5208121d112ad8fc90 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 28 Jul 2023 00:02:58 +0200 Subject: [PATCH 05/10] Make lint happy --- CHANGELOG.md | 2 ++ lib/WorkflowAtacseq.groovy | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 09c6c298..2106e64e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,9 +4,11 @@ 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). ## 2.1.2dev - [date] + ### Enhancements & fixes - Remove fasta from required schema parameter so that when launching from tools it is not required. +- Update `homer_annotatepeaks` module. ## [[2.1.1](https://github.com/nf-core/atacseq/releases/tag/2.1.1)] - 2022-07-21 diff --git a/lib/WorkflowAtacseq.groovy b/lib/WorkflowAtacseq.groovy index b4dcae39..663df1fb 100755 --- a/lib/WorkflowAtacseq.groovy +++ b/lib/WorkflowAtacseq.groovy @@ -16,7 +16,7 @@ class WorkflowAtacseq { 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) From 2295815f591be00d529ffe5f85f920270c7174bf Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 28 Jul 2023 09:39:52 +0200 Subject: [PATCH 06/10] Update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2106e64e..1be51e44 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Enhancements & fixes -- Remove fasta from required schema parameter so that when launching from tools it is not required. +- [[#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. - Update `homer_annotatepeaks` module. ## [[2.1.1](https://github.com/nf-core/atacseq/releases/tag/2.1.1)] - 2022-07-21 From 28183e87bf86a44d2acbcf53a45ba01a24eac050 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 28 Jul 2023 17:26:22 +0200 Subject: [PATCH 07/10] Bump version 2.1.2 --- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1be51e44..49b5fa47 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## 2.1.2dev - [date] +## [[2.1.2](https://github.com/nf-core/atacseq/releases/tag/2.1.2)] - 2022-07-28 ### Enhancements & fixes diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f902256a..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/nextflow.config b/nextflow.config index 7fc83c34..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 = '2.2.0dev' + version = '2.1.2' doi = 'https://doi.org/10.5281/zenodo.2634132' } From c17a7a164560e22366cc996b12284738874faec6 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 31 Jul 2023 16:40:25 +0200 Subject: [PATCH 08/10] Update release date --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 49b5fa47..3e4e94e5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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)] - 2022-07-28 +## [[2.1.2](https://github.com/nf-core/atacseq/releases/tag/2.1.2)] - 2022-07-31 ### Enhancements & fixes From aa9d66b86d0c77a48955bb4e2cf049368365e24d Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 7 Aug 2023 09:21:42 +0200 Subject: [PATCH 09/10] Update release date --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e4e94e5..ca35582e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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)] - 2022-07-31 +## [[2.1.2](https://github.com/nf-core/atacseq/releases/tag/2.1.2)] - 2022-08-07 ### Enhancements & fixes From ce83f78c90b82b7e4dbcb595b375a4308b017b38 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 7 Aug 2023 09:35:02 +0200 Subject: [PATCH 10/10] Fix typo --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ca35582e..f5fd84c8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### 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. -- Update `homer_annotatepeaks` module. +- Updates `homer_annotatepeaks` module. ## [[2.1.1](https://github.com/nf-core/atacseq/releases/tag/2.1.1)] - 2022-07-21