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Merge pull request #57 from nf-core/dev
2.1.0 release
2 parents 9ed7c7b + 0420389 commit 9b5fd10

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‎.github/workflows/awsfulltest.yml‎

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@@ -4,44 +4,23 @@ name: nf-core AWS full size tests
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# It runs the -profile 'test_full' on AWS batch
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on:
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pull_request:
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branches:
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- main
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- master
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workflow_dispatch:
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pull_request_review:
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types: [submitted]
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release:
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types: [published]
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jobs:
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run-platform:
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name: Run AWS full tests
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# run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
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if: github.repository == 'nf-core/pairgenomealign' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
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# run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
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if: github.repository == 'nf-core/pairgenomealign' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
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runs-on: ubuntu-latest
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steps:
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- name: Get PR reviews
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uses: octokit/request-action@v2.x
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if: github.event_name != 'workflow_dispatch'
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id: check_approvals
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continue-on-error: true
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with:
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route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Check for approvals
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if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
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run: |
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echo "No review approvals found. At least 2 approvals are required to run this action automatically."
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exit 1
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- name: Check for enough approvals (>=2)
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id: test_variables
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if: github.event_name != 'workflow_dispatch'
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- name: Set revision variable
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id: revision
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run: |
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JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
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CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
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test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
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echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
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- name: Launch workflow via Seqera Platform
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uses: seqeralabs/action-tower-launch@v2
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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revision: ${{ github.sha }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/pairgenomealign/work-${{ github.sha }}
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revision: ${{ steps.revision.outputs.revision }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/pairgenomealign/work-${{ steps.revision.outputs.revision }}
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/pairgenomealign/results-${{ github.sha }}"
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/pairgenomealign/results-${{ steps.revision.outputs.revision }}"
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}
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profiles: test_full
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‎.github/workflows/ci.yml‎

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uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
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- name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
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continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results

‎.nf-core.yml‎

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lint:
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files_unchanged:
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- assets/nf-core-pairgenomealign_logo_light.png
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- docs/images/nf-core-pairgenomealign_logo_light.png
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- docs/images/nf-core-pairgenomealign_logo_dark.png
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nf_core_version: 3.2.0
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nf_core_version: 3.2.1
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repository_type: pipeline
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template:
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author: charles-plessy

‎CHANGELOG.md‎

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [v2.1.0](https://github.com/nf-core/pairgenomealign/releases/tag/2.1.0) "Goya champuru" - [May 16th 2025]
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### `Added`
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- New `--dotplot_filter` paramater to produce extra alignment plots where small off-diagonal signal is filtered out ([#35](https://github.com/nf-core/pairgenomealign/issues/35)).
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- New `--dotplot_width`, `--dotplot_height` and `--dotplot_font_size` parameters to control alignment plot size ([#38](https://github.com/nf-core/pairgenomealign/issues/38)).
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### `Fixed`
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- In alignment plots, contig names are now written with a nice scalable font instead of being pixellised ([#44](https://github.com/nf-core/pairgenomealign/issues/44)).
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- Conforms to nf-core template version 3.2.1 ([#54](https://github.com/nf-core/pairgenomealign/pull/54)).
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- Removed some old linting exceptions.
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- Removed the `gfastats` modules, which was actually not used.
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- Make sure the subworkflows collect all module versions.
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- Fix plot IDs for comptatibility with MultiQC 1.28.
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### `Parameters`
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| Old parameter | New parameter |
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| ------------- | --------------------- |
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| | `--dotplot_filter` |
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| | `--dotplot_font_size` |
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| | `--dotplot_height` |
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| | `--dotplot_width` |
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### `Dependencies`
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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| `LAST` | 1608 | 1611 |
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| `MultiQC` | 1.27 | 1.28 |
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## [v2.0.0](https://github.com/nf-core/pairgenomealign/releases/tag/2.0.0) "Naga imo" - [February 5th, 2025]
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### `Breaking changes`

‎assets/multiqc_config.yml‎

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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/releases/tag/2.0.0"
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This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/releases/tag/2.1.0"
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target="_blank">nf-core/pairgenomealign</a> analysis pipeline. For information about
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how to interpret these results, please see the <a href="https://nf-co.re/pairgenomealign/2.0.0/docs/output"
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how to interpret these results, please see the <a href="https://nf-co.re/pairgenomealign/2.1.0/docs/output"
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target="_blank">documentation</a>.
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report_section_order:
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"nf-core-pairgenomealign-methods-description":

‎assets/nf-core-pairgenomealign_logo_light.png‎

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‎conf/modules.config‎

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withName: 'LAST_DOTPLOT' {
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// The number one cause of failure is absence of alignments.
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errorStrategy = { task.exitStatus in (130..145) ? 'retry' : task.exitStatus == 1 ? 'ignore' : 'finish' }
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ext.args = { "--rot2=h --sort2=3 --strands2=1 ${params.dotplot_options}" }
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ext.args = { "--rot2=h --sort2=3 --strands2=1 --width=${params.dotplot_width} --height=${params.dotplot_height} --fontsize=${params.dotplot_font_size} ${params.dotplot_options}" }
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}
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withName: 'ALIGNMENT_DOTPLOT_O2O' {
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ext.prefix = { "${meta.id}.m2m_plt" }
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}
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withName: 'ALIGNMENT_DOTPLOT_O2O_FLT' {
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ext.prefix = { "${meta.id}.o2o_plt_filtered" }
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}
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withName: 'ALIGNMENT_DOTPLOT_M2O_FLT' {
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ext.prefix = { "${meta.id}.m2o_plt_filtered" }
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}
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withName: 'ALIGNMENT_DOTPLOT_O2M_FLT' {
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ext.prefix = { "${meta.id}.o2m_plt_filtered" }
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}
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withName: 'ALIGNMENT_DOTPLOT_M2M_FLT' {
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ext.prefix = { "${meta.id}.m2m_plt_filtered" }
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}
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withName: 'MULTIQC' {
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ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
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publishDir = [

‎conf/test.config‎

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target = params.pipelines_testdata_base_path + 'modules/data/genomics/sarscov2/genome/genome.fasta'
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lastal_args = '-C2' // Remove -D1e9 because the virus genomes are so small.
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// Also test aligmnment export
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export_aln_to = 'sam'
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// Genome references
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genome = 'R64-1-1'
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}

‎docs/output.md‎

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</details>
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Dot plots representing the pairwise genome alignments, produced with the [`last-dotplot`](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst) tool. In the one-to-one alignment example below, the `hg38` human genome (_target_) is represented on the horizontal axis and a monkey genopme (_Macaca mulatta_ accession number `GCA\_003339765.3`) on the vertical axis (_query_). Regions containing unknown (`N`) sequences are on pink background. Forward (+/+) alignments are plotted in red and reverse (+/– or –/+) in blue. _Target_ (human) contigs are displayed in their original order. _Query_ contigs (monkey) are reordered and possibly reverse-complemented to diagonalise the plot as much as possible. The names of reverse-complemented contigs are printed in blue.
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Dot plots are representing the pairwise genome alignments and produced with the [`last-dotplot`](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst) tool. By default, their maximal width is fixed to aproximately 1000 pixels, so that the _target_ genome is always represented at the same scale in all plots. In the one-to-one alignment example below, the `hg38` human genome (_target_) is represented on the horizontal axis and a monkey genopme (_Macaca mulatta_ accession number `GCA\_003339765.3`) on the vertical axis (_query_). Regions containing unknown (`N`) sequences are on pink background. Forward (+/+) alignments are plotted in red and reverse (+/– or –/+) in blue. _Target_ (human) contigs are displayed in their original order. _Query_ contigs (monkey) are reordered and possibly reverse-complemented to diagonalise the plot as much as possible. The names of reverse-complemented contigs are printed in blue.
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![Example of a dot-plot produced by the pipeline after aligning human and macaque genomes](images/Homo_sapiens_GCA_000001405.29_GRCh38.p14___Macaca_mulatta_GCA_003339765.3.o2o_plt.png "Human–Monkey comparison")
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‎modules.json‎

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"nf-core": {
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"assemblyscan": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"installed_by": ["modules"]
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},
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"gfastats": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"last/dotplot": {
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"branch": "master",
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"git_sha": "b651d72024027c922b5014aec80add091df63831",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"last/lastal": {
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"branch": "master",
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"git_sha": "b651d72024027c922b5014aec80add091df63831",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"last/lastdb": {
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"branch": "master",
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"git_sha": "b651d72024027c922b5014aec80add091df63831",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"last/mafconvert": {
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"branch": "master",
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"git_sha": "b651d72024027c922b5014aec80add091df63831",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"last/mafswap": {
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"branch": "master",
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"git_sha": "b651d72024027c922b5014aec80add091df63831",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"last/split": {
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"branch": "master",
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"git_sha": "b651d72024027c922b5014aec80add091df63831",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"last/train": {
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"branch": "master",
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"git_sha": "29a99284f30fa0c5fd0f5dca192c94b80de0be30",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
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"git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
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"installed_by": ["modules"]
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},
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"seqtk/cutn": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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}
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}

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