diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index d1d686b..2980b4f 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -1,15 +1,15 @@ name: nf-core branch protection -# This workflow is triggered on PRs to master branch on the repository -# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` +# This workflow is triggered on PRs to main branch on the repository +# It fails when someone tries to make a PR against the Plant-Food-Research-Open `main` branch instead of `dev` on: pull_request_target: - branches: [master] + branches: [main] jobs: test: runs-on: ubuntu-latest steps: - # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches + # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - name: Check PRs if: github.repository == 'Plant-Food-Research-Open/genepal' run: | @@ -22,7 +22,7 @@ jobs: uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | - ## This PR is against the `master` branch :x: + ## This PR is against the `main` branch :x: * Do not close this PR * Click _Edit_ and change the `base` to `dev` @@ -32,9 +32,9 @@ jobs: Hi @${{ github.event.pull_request.user.login }}, - It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. - The `master` branch on nf-core repositories should always contain code from the latest release. - Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. + It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `main` branch. + The `main` branch should always contain code from the latest release. + Because of this, PRs to `main` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit. diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 713dc3e..7cc2c38 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually -# - when a PR is opened or reopened to master branch +# - when a PR is opened or reopened to main branch # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: @@ -17,10 +17,10 @@ on: - edited - synchronize branches: - - master + - main pull_request_target: branches: - - master + - main env: NXF_ANSI_LOG: false diff --git a/.nf-core.yml b/.nf-core.yml index 260014a..1332478 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -30,5 +30,5 @@ template: outdir: . skip_features: - igenomes - version: 0.5.0 + version: 0.5.1 update: null diff --git a/CHANGELOG.md b/CHANGELOG.md index 79627bc..f301e35 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,22 @@ 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). +## v0.5.1 - [02-Dec-2024] + +### `Added` + +### `Fixed` + +1. Fixed an issue where TSEBRA failed because LIFTOFF mislabelled the phase of CDS features [#115](https://github.com/Plant-Food-Research-Open/genepal/issues/115) +2. Switched branch name from `master` to `main` in the GHA CIs + +### `Dependencies` + +1. Nextflow!>=24.04.2 +2. nf-schema@2.1.1 + +### `Deprecated` + ## v0.5.0 - [21-Nov-2024] ### `Added` diff --git a/CITATION.cff b/CITATION.cff index c5c6c26..8535f45 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -31,7 +31,7 @@ authors: - family-names: "Thomson" given-names: "Susan" title: "genepal: A Nextflow pipeline for genome and pan-genome annotation" -version: 0.5.0 +version: 0.5.1 date-released: 2024-11-21 url: "https://github.com/Plant-Food-Research-Open/genepal" doi: 10.5281/zenodo.14195006 diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 8969c04..8c0242c 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > This report has been generated by the plant-food-research-open/genepal analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "plant-food-research-open-genepal-methods-description": diff --git a/conf/modules.config b/conf/modules.config index ba2bb72..5af19c6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -215,6 +215,11 @@ process { // SUBWORKFLOW: FASTA_LIFTOFF ext.args = '--keep-genes' } + withName: '.*:FASTA_LIFTOFF:GT_GFF3_AFTER_LIFTOFF' { + ext.prefix = { "${meta.id}.liftoff.fixed" } + ext.args = '-tidy -retainids -sort -addids no' + } + withName: '.*:FASTA_LIFTOFF:GFF_TSEBRA_SPFILTERFEATUREFROMKILLLIST:AGAT_CONVERTSPGFF2GTF' { ext.args = '--gtf_version relax' } diff --git a/nextflow.config b/nextflow.config index 665e6b3..b0aef4d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -261,7 +261,7 @@ manifest { description = """A Nextflow pipeline for consensus, phased and pan-genome annotation.""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '0.5.0' + version = '0.5.1' doi = 'https://doi.org/10.5281/zenodo.14195006' } diff --git a/subworkflows/local/fasta_liftoff.nf b/subworkflows/local/fasta_liftoff.nf index 0da2949..8475616 100644 --- a/subworkflows/local/fasta_liftoff.nf +++ b/subworkflows/local/fasta_liftoff.nf @@ -6,6 +6,7 @@ include { AGAT_SPMERGEANNOTATIONS as MERGE_LIFTOFF_ANNOTATIONS } from '../../mo include { AGAT_SPFLAGSHORTINTRONS } from '../../modules/gallvp/agat/spflagshortintrons/main' include { AGAT_SPFILTERFEATUREFROMKILLLIST } from '../../modules/nf-core/agat/spfilterfeaturefromkilllist/main' include { GFFREAD as GFFREAD_AFTER_LIFTOFF } from '../../modules/nf-core/gffread/main' +include { GT_GFF3 as GT_GFF3_AFTER_LIFTOFF } from '../../modules/nf-core/gt/gff3/main' include { GFF_TSEBRA_SPFILTERFEATUREFROMKILLLIST } from '../../subworkflows/local/gff_tsebra_spfilterfeaturefromkilllist' workflow FASTA_LIFTOFF { @@ -120,8 +121,8 @@ workflow FASTA_LIFTOFF { ch_versions = ch_versions.mix(AGAT_SPFLAGSHORTINTRONS.out.versions.first()) // COLLECTFILE: Kill list for valid_ORF=False transcripts - // tRNA, rRNA - // gene with any intron marked as 'pseudo=' by AGAT/SPFLAGSHORTINTRONS + // tRNA, rRNA, gene with any intron marked as + // 'pseudo=' by AGAT/SPFLAGSHORTINTRONS ch_kill_list = ch_flagged_gff | map { meta, gff -> @@ -171,9 +172,16 @@ workflow FASTA_LIFTOFF { // MODULE: GFFREAD as GFFREAD_AFTER_LIFTOFF GFFREAD_AFTER_LIFTOFF ( ch_liftoff_purged_gff, [] ) - ch_attr_trimmed_gff = GFFREAD_AFTER_LIFTOFF.out.gffread_gff ch_versions = ch_versions.mix(GFFREAD_AFTER_LIFTOFF.out.versions.first()) + // MODULE: GT_GFF3 as GT_GFF3_AFTER_LIFTOFF + // To fix the phase mislabelled by LIFTOFF + // https://github.com/Plant-Food-Research-Open/genepal/issues/115 + GT_GFF3_AFTER_LIFTOFF ( GFFREAD_AFTER_LIFTOFF.out.gffread_gff ) + + ch_attr_trimmed_gff = GT_GFF3_AFTER_LIFTOFF.out.gt_gff3 + ch_versions = ch_versions.mix(GT_GFF3_AFTER_LIFTOFF.out.versions.first()) + // SUBWORKFLOW: GFF_TSEBRA_SPFILTERFEATUREFROMKILLLIST GFF_TSEBRA_SPFILTERFEATUREFROMKILLLIST( val_filter_liftoff_by_hints ? ch_attr_trimmed_gff : Channel.empty(), diff --git a/tests/minimal/main.nf.test.snap b/tests/minimal/main.nf.test.snap index 02c228f..79a46b9 100644 --- a/tests/minimal/main.nf.test.snap +++ b/tests/minimal/main.nf.test.snap @@ -55,7 +55,7 @@ "tsebra": "1.1.2.5" }, "Workflow": { - "plant-food-research-open/genepal": "v0.5.0" + "plant-food-research-open/genepal": "v0.5.1" } }, "stable paths": [ @@ -82,8 +82,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.10.1" }, - "timestamp": "2024-11-19T11:35:02.477202" + "timestamp": "2024-12-02T16:52:30.400922" } -} +} \ No newline at end of file diff --git a/tests/short/main.nf.test.snap b/tests/short/main.nf.test.snap index 62a4ed3..e9f7331 100644 --- a/tests/short/main.nf.test.snap +++ b/tests/short/main.nf.test.snap @@ -5,18 +5,18 @@ "successful tasks": 0, "versions": { "Workflow": { - "plant-food-research-open/genepal": "v0.5.0" + "plant-food-research-open/genepal": "v0.5.1" } }, "stable paths": [ - + ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.10.1" }, - "timestamp": "2024-10-22T11:39:43.110621" + "timestamp": "2024-12-02T16:52:41.687179" } -} +} \ No newline at end of file diff --git a/tests/stub/main.nf.test.snap b/tests/stub/main.nf.test.snap index 524ce21..82efa9c 100644 --- a/tests/stub/main.nf.test.snap +++ b/tests/stub/main.nf.test.snap @@ -2,7 +2,7 @@ "full - stub": { "content": [ { - "successful tasks": 154, + "successful tasks": 158, "versions": { "AGAT_CONVERTSPGFF2GTF": { "agat": "v1.4.0" @@ -79,6 +79,9 @@ "GT_GFF3": { "genometools": "1.6.5" }, + "GT_GFF3_AFTER_LIFTOFF": { + "genometools": "1.6.5" + }, "GUNZIP": { "gunzip": 1.1 }, @@ -143,7 +146,7 @@ "tsebra": "1.1.2.5" }, "Workflow": { - "plant-food-research-open/genepal": "v0.5.0" + "plant-food-research-open/genepal": "v0.5.1" } }, "stable paths": [ @@ -191,6 +194,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-11-21T12:34:14.056074" + "timestamp": "2024-12-02T17:01:15.438026" } -} +} \ No newline at end of file