From d8f540c1c027d3b07d91a222c586a94782989709 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 1 Sep 2026 12:59:03 +0000 Subject: [PATCH 1/8] Template update for nf-core/tools version 4.1.0 --- .github/actions/nf-test/action.yml | 6 +- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 6 +- .github/workflows/fix_linting.yml | 6 +- .github/workflows/linting.yml | 16 +- .github/workflows/nf-test.yml | 4 +- .../workflows/template-version-comment.yml | 2 +- .hooks/block_pipeline_outdir.sh | 44 + .nf-core.yml | 5 +- .pre-commit-config.yaml | 19 +- CHANGELOG.md | 2 +- README.md | 2 +- conf/base.config | 3 + conf/containers_conda_lock_files_amd64.config | 2 +- conf/containers_conda_lock_files_arm64.config | 2 +- conf/containers_docker_amd64.config | 2 +- conf/containers_docker_arm64.config | 2 +- .../containers_singularity_https_amd64.config | 2 +- .../containers_singularity_https_arm64.config | 2 +- conf/containers_singularity_oras_amd64.config | 2 +- conf/containers_singularity_oras_arm64.config | 2 +- conf/modules.config | 3 +- docs/CONTRIBUTING.md | 8 +- docs/output.md | 2 +- docs/usage.md | 2 +- modules.json | 6 +- .../linux_amd64-bd-c17fb751507e9dfc_1.txt | 1526 +++++++++++++++++ .../linux_arm64-bd-5c84a5000a226ab5_1.txt | 1476 ++++++++++++++++ modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- modules/nf-core/multiqc/meta.yml | 28 +- .../nf-core/multiqc/tests/main.nf.test.snap | 10 +- ro-crate-metadata.json | 14 +- .../main.nf | 3 +- .../nf-core/utils_nfschema_plugin/main.nf | 12 +- .../nf-core/utils_nfschema_plugin/meta.yml | 24 + .../utils_nfschema_plugin/tests/main.nf.test | 5 + .../tests/nextflow.config | 2 +- tests/nextflow.config | 5 +- 39 files changed, 3184 insertions(+), 81 deletions(-) create mode 100755 .hooks/block_pipeline_outdir.sh create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 945c56f..4175e3c 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -20,12 +20,12 @@ runs: using: "composite" steps: - name: Setup Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 with: version: "${{ env.NXF_VERSION }}" - name: Set up Python - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: python-version: "3.14" @@ -37,7 +37,7 @@ runs: - name: Setup apptainer if: contains(inputs.profile, 'singularity') - uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 + uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2.0.0 - name: Set up Singularity if: contains(inputs.profile, 'singularity') diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 172de6f..b694012 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10 + - uses: actions/stale@4391f3da665fdf50b6810c1a66712fb9ba21aa93 # v11 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index a7bf4fc..ca2eb82 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -39,15 +39,15 @@ jobs: needs: configure steps: - name: Check out pipeline code - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: python-version: "3.14" architecture: "x64" diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index 3d6fa6c..254c304 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,12 +32,12 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 # Install and run prek - name: Run prek id: prek - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 continue-on-error: true # indication that the linting has finished diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index bc32219..277f12f 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,30 +11,30 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - name: Run prek - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 nf-core: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: python-version: "3.14" architecture: "x64" - name: Setup uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: read .nf-core.yml uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 @@ -46,7 +46,7 @@ jobs: run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Run nf-core pipelines lint - if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} + if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 4de681a..e363215 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -40,7 +40,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: fetch-depth: 0 @@ -85,7 +85,7 @@ jobs: TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: fetch-depth: 0 diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index ee102f7..149e285 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: ref: ${{ github.event.pull_request.head.sha }} diff --git a/.hooks/block_pipeline_outdir.sh b/.hooks/block_pipeline_outdir.sh new file mode 100755 index 0000000..e9ba4f9 --- /dev/null +++ b/.hooks/block_pipeline_outdir.sh @@ -0,0 +1,44 @@ +#!/usr/bin/env bash +# This hook is used to block commits if they include staged files inside a directory +# which also contains a subdirectory called `pipeline_info`. The purpose of this is to +# prevent users from inadvertently committing output from pipeline test runs inside the +# development directory. + +set -e + +status=0 +seen_dirs="" + +while IFS= read -r file; do + # The offending output bundle's root is the ancestor directory that has + # `pipeline_info` as an immediate child, so callers can restore it in one go. + if [[ "$file" == pipeline_info/* ]]; then + top_dir="pipeline_info" + elif [[ "$file" == */pipeline_info/* ]]; then + top_dir="${file%%/pipeline_info/*}" + else + top_dir="" + dir=$(dirname "$file") + while [[ "$dir" != "." && "$dir" != "/" ]]; do + if [[ -d "$dir/pipeline_info" ]]; then + top_dir="$dir" + break + fi + dir=$(dirname "$dir") + done + fi + + if [[ -n "$top_dir" ]]; then + echo "❌ Commit blocked: Please do not commit output from pipeline test runs to the pipeline code itself: $file" + status=1 + case "$seen_dirs" in + *"|$top_dir|"*) ;; + *) + echo "Run 'git restore --staged $top_dir' to remove the whole output folder from the staging area." + seen_dirs="$seen_dirs|$top_dir|" + ;; + esac + fi +done < <(git diff --cached --name-only) + +exit "$status" diff --git a/.nf-core.yml b/.nf-core.yml index f11e683..594af75 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -3,12 +3,15 @@ lint: - .github/workflows/ci.yml - conf/igenomes.config - conf/igenomes_ignored.config + - .github/workflows/linting_comment.yml files_unchanged: - assets/nf-core-proteinannotator_logo_light.png - docs/images/nf-core-proteinannotator_logo_light.png - docs/images/nf-core-proteinannotator_logo_dark.png - .github/PULL_REQUEST_TEMPLATE.md -nf_core_version: 4.0.3 + - .github/workflows/branch.yml + - .github/workflows/linting.yml +nf_core_version: 4.1.0 repository_type: pipeline template: author: Olga Botvinnik, Evangelos Karatzas diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f51e1a2..e9503db 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.8.3 + - prettier@3.9.6 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: @@ -25,9 +25,26 @@ repos: subworkflows/(?!local/).*| .*\.snap$ )$ + - id: check-added-large-files + args: [--maxkb=5000] + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + .*\.snap$| + lib/nfcore_external_java_deps.jar$| + docs/.*\.(svg|pdf)$| + assets/.*$ + )$ + - id: check-merge-conflict - repo: https://github.com/seqeralabs/nf-lint-pre-commit rev: v0.3.0 hooks: - id: nextflow-lint files: '\.nf$|nextflow\.config$' args: ["-output", "json"] + - repo: local + hooks: + - id: block-pipeline-outdir + name: Prevent committing output from pipeline test runs to the pipeline code itself + entry: ./.hooks/block_pipeline_outdir.sh + language: script diff --git a/CHANGELOG.md b/CHANGELOG.md index 97805f8..4e49654 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). -## v1.2.0dev - [date] +## v1.2.0dev - [unreleased] Initial release of nf-core/proteinannotator, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index 86d0be2..2118e32 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.3-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.3) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/conf/base.config b/conf/base.config index 7212d70..4152257 100644 --- a/conf/base.config +++ b/conf/base.config @@ -49,6 +49,9 @@ process { withLabel:process_long { time = { 20.h * task.attempt } } + withLabel:process_low_memory { + memory = { 1.GB * task.attempt } + } withLabel:process_high_memory { memory = { 200.GB * task.attempt } } diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config index f487ba4..eb32fe5 100644 --- a/conf/containers_conda_lock_files_amd64.config +++ b/conf/containers_conda_lock_files_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } } +process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } } diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config index e9a3fed..3733ddf 100644 --- a/conf/containers_conda_lock_files_arm64.config +++ b/conf/containers_conda_lock_files_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } } +process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } } diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config index 01b59df..ea18c3f 100644 --- a/conf/containers_docker_amd64.config +++ b/conf/containers_docker_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } } diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config index 7785cb1..369f743 100644 --- a/conf/containers_docker_arm64.config +++ b/conf/containers_docker_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } } diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config index 754821b..932fc7c 100644 --- a/conf/containers_singularity_https_amd64.config +++ b/conf/containers_singularity_https_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } } +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } } diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config index 93071de..4f79532 100644 --- a/conf/containers_singularity_https_arm64.config +++ b/conf/containers_singularity_https_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } } +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } } diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config index 952881d..2fa065b 100644 --- a/conf/containers_singularity_oras_amd64.config +++ b/conf/containers_singularity_oras_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } } +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } } diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config index 498ec50..84f0792 100644 --- a/conf/containers_singularity_oras_arm64.config +++ b/conf/containers_singularity_oras_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } } +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } } diff --git a/conf/modules.config b/conf/modules.config index f0b0d55..c50e0b7 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -22,8 +22,7 @@ process { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ path: { "${params.outdir}/multiqc" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + mode: params.publish_dir_mode ] } diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index a97d0b7..04e8dfa 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -40,12 +40,12 @@ The nf-core stance on the use of AI and LLMs is that humans are still ultimately If you’re using AI tools, try to stick by these guidelines: -- Keep PRs as small and focussed as possible +- Keep PRs as small and focused as possible - Avoid any unnecessary changes, such as moving or refactoring code (unless that is the explicit intention of the PR) - Review all generated code yourself before opening a PR, and ensure that you understand it - Engage with the community review process and expect to make revisions -For more detail, see the the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team. +For more detail, see the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team. ### Getting help @@ -128,7 +128,7 @@ Please also refer to the [pipeline-specific contribution guidelines](#pipeline-s - [ ] Perform local tests to validate that the new code works as expected. - [ ] If applicable, add a new test in the `tests` directory. - [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate. -- [ ] [Lint](lint) the code with nf-core/tools. +- [ ] [Lint](#lint-tests) the code with nf-core/tools. - [ ] Update any diagrams or pipeline images as necessary. - [ ] Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name cleanup, and module plots are in the appropriate order. - [ ] If applicable, create a [MultiQC](https://seqera.io/multiqc/) module. @@ -166,7 +166,7 @@ Specify these with generic `withLabel:` selectors, so they can be shared across nf-core provides a set of standard labels that you should follow where possible, as seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config). These labels define resource defaults for single-core processes, modules that require a GPU, and different levels of multi-core configurations with increasing memory requirements. -Values assigned within these labels can be dynamically passed to a tool using the the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)). +Values assigned within these labels can be dynamically passed to a tool using the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)). #### Nextflow version bumping diff --git a/docs/output.md b/docs/output.md index c3d4a88..6a3c3d3 100644 --- a/docs/output.md +++ b/docs/output.md @@ -44,4 +44,4 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ -[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. +[Nextflow](https://docs.seqera.io/platform-cloud/reports/overview) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. diff --git a/docs/usage.md b/docs/usage.md index 019d4cc..27e5216 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -152,7 +152,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `wave` - - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). + - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow `24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. diff --git a/modules.json b/modules.json index 7ee1ced..668e3aa 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "multiqc": { "branch": "master", - "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", + "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade", "installed_by": ["modules"] } } @@ -16,7 +16,7 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { @@ -26,7 +26,7 @@ }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57", + "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436", "installed_by": ["subworkflows"] } } diff --git 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b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.34 + - bioconda::multiqc=1.35 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index e80e8cd..c4bc715 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -4,8 +4,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' - : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' + : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}" input: tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 2facc62..27ce18d 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -110,24 +110,24 @@ maintainers: containers: conda: linux/amd64: - lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt linux/arm64: - lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt docker: linux/amd64: - name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6 - build_id: bd-db7c73dae76bc9e6_1 - scan_id: sc-66fc7138dbf1cf48_1 + name: community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc + build_id: bd-c17fb751507e9dfc_1 + scan_id: sc-3b1b3932f9846892_1 linux/arm64: - name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136 - build_id: bd-d167b8012595a136_1 - scan_id: sc-ac701dfa631a2af9_1 + name: community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5 + build_id: bd-5c84a5000a226ab5_1 + scan_id: sc-0d39df41e9737bbd_1 singularity: linux/amd64: - name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0 - build_id: bd-4fc8657c816047c0_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data + name: oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2 + build_id: bd-c680f2aea25ccec2_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data linux/arm64: - name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726 - build_id: bd-7fbd82d945c06726_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data + name: oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81 + build_id: bd-c0468833d65b2f81_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7c2f370..4489921 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -81,7 +81,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -175,7 +175,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -221,7 +221,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -314,7 +314,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -408,7 +408,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 735d293..ad333d0 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2026-07-24T12:36:11+00:00", - "description": "

\n \n \n \"nf-core/proteinannotator\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/proteinannotator)\n[![GitHub Actions CI Status](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.3-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.3)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinannotator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23proteinannotator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/proteinannotator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/proteinannotator** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/proteinannotator \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/proteinannotator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/proteinannotator/output).\n\n## Credits\n\nnf-core/proteinannotator was originally written by Olga Botvinnik, Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2026-09-01T12:58:59+00:00", + "description": "

\n \n \n \"nf-core/proteinannotator\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/proteinannotator)\n[![GitHub Actions CI Status](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinannotator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23proteinannotator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/proteinannotator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/proteinannotator** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/proteinannotator \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/proteinannotator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/proteinannotator/output).\n\n## Credits\n\nnf-core/proteinannotator was originally written by Olga Botvinnik, Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#298e589a-490b-4612-aa89-ca4366da3a32" + "@id": "#b1c0b828-9db5-4bbd-94a0-ffe1d7e49a89" } ], "name": "nf-core/proteinannotator" @@ -131,7 +131,7 @@ } ], "dateCreated": "", - "dateModified": "2026-07-24T12:36:11Z", + "dateModified": "2026-09-01T12:58:59Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": ["nf-core", "nextflow", "annotation", "proteomics"], "license": ["MIT"], @@ -158,11 +158,11 @@ "version": "!>=25.10.4" }, { - "@id": "#298e589a-490b-4612-aa89-ca4366da3a32", + "@id": "#b1c0b828-9db5-4bbd-94a0-ffe1d7e49a89", "@type": "TestSuite", "instance": [ { - "@id": "#ba41f42b-de31-45cc-b1f8-751ccec12108" + "@id": "#6cd80838-6920-4883-a7a4-3e2bafb938f0" } ], "mainEntity": { @@ -171,7 +171,7 @@ "name": "Test suite for nf-core/proteinannotator" }, { - "@id": "#ba41f42b-de31-45cc-b1f8-751ccec12108", + "@id": "#6cd80838-6920-4883-a7a4-3e2bafb938f0", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/proteinannotator", "resource": "repos/nf-core/proteinannotator/actions/workflows/nf-test.yml", diff --git a/subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf b/subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf index 00ff34b..5981785 100644 --- a/subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf @@ -88,7 +88,8 @@ workflow PIPELINE_INITIALISATION { show_hidden, before_text, after_text, - command + command, + false ) // diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index 1df8b76..9ff0681 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -22,6 +22,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { before_text // string: text to show before the help message and parameters summary after_text // string: text to show after the help message and parameters summary command // string: an example command of the pipeline + cli_typecast // boolean: whether to perform typecasting of CLI parameters. Set this to `null` to use the default behaviour main: @@ -34,11 +35,11 @@ workflow UTILS_NFSCHEMA_PLUGIN { fullHelp: help_full, ] if(parameters_schema) { - help_options << [parametersSchema: parameters_schema] + help_options << [parameters_schema: parameters_schema] } log.info paramsHelp( help_options, - (params.help instanceof String && params.help != "true") ? params.help : "", + (help instanceof String && help != "true") ? help : "", ) exit 0 } @@ -50,7 +51,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { summary_options = [:] if(parameters_schema) { - summary_options << [parametersSchema: parameters_schema] + summary_options << [parameters_schema: parameters_schema] } log.info before_text log.info paramsSummaryLog(summary_options, input_workflow) @@ -63,7 +64,10 @@ workflow UTILS_NFSCHEMA_PLUGIN { if(validate_params) { validateOptions = [:] if(parameters_schema) { - validateOptions << [parametersSchema: parameters_schema] + validateOptions << [parameters_schema: parameters_schema] + } + if(cli_typecast != null) { + validateOptions << [cast_cli_params: cli_typecast] } validateParameters(validateOptions) } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml index f7d9f02..1d8c75a 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -25,6 +25,30 @@ input: option. When this input is empty it will automatically use the configured schema or "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way for meta pipelines. + - help: + type: boolean, string + description: | + Show the help message and exit. When a parameter name is given, show the help message for that parameter instead of the general help message. + - help_full: + type: boolean + description: Show the full help message and exit. + - show_hidden: + type: boolean + description: Show hidden parameters in the help message. + - before_text: + type: string + description: Text to show before the parameters summary and help message. + - after_text: + type: string + description: Text to show after the parameters summary and help message. + - command: + type: string + description: An example command to run the pipeline, to show in the help message and the summary. + - cli_typecast: + type: boolean + description: | + Whether to apply typecasting to the parameters given via the CLI before validation. + Set this to `null` to use the default behavior. output: - dummy_emit: type: boolean diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index c977917..1fd1eac 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -63,6 +64,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -95,6 +97,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -127,6 +130,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -160,6 +164,7 @@ nextflow_workflow { input[6] = "Before" input[7] = "After" input[8] = "nextflow run test/test" + input[9] = null """ } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index f6537cc..fd71cb8 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.6.1" + id "nf-schema@2.7.2" } validation { diff --git a/tests/nextflow.config b/tests/nextflow.config index 0a73751..13b0afc 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -8,7 +8,8 @@ // Or any resources requirements params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/proteinannotator/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinannotator/' } -aws.client.anonymous = true // fixes S3 access issues on self-hosted runners +// Fixes S3 access issues on self-hosted runners +aws.client.anonymous = true From b088c3e9013c89994edeed15d803ebd4392aec29 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Wed, 2 Sep 2026 11:04:00 +0100 Subject: [PATCH 2/8] wip rocrate update --- ro-crate-metadata.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 467a92b..89380a6 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2026-07-24T12:36:11+00:00", - "description": "

\n \n \n \"nf-core/proteinannotator\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/proteinannotator)\n[![GitHub Actions CI Status](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.18547735-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.18547735)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.3-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.3)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinannotator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23proteinannotator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/proteinannotator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/proteinannotator** is a bioinformatics pipeline that computes statistics for protein FASTA inputs and produces protein annotations based on predicted sequence features, including conserved domains, functions, and secondary structure.\n\n

\n \n \n \"nf-core/proteinannotator\"\n \n

\n\n### Check quality and pre-process\n\nGenerate input amino acid sequence statistics with ([`SeqFu`](https://github.com/telatin/seqfu2/)) and pre-process them (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences) with ([`SeqKit`](https://github.com/shenwei356/seqkit/))\n\n### Annotate sequences\n\n1. Conserved domain annotation with ([`hmmer`](https://github.com/EddyRivasLab/hmmer/)) against databases\n such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/), [FunFam](https://download.cathdb.info/cath/releases/all-releases/), and [NMPFams and metagRoot](https://pavlopoulos-lab.org/envofams/databases/hmmer/)\n2. Functional annotation:\n - ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.\n - ([`KOfamScan`](https://github.com/takaram/kofam_scan)) assigns KEGG Orthologs to protein sequences using profile HMMs and KO-specific score thresholds.\n3. Predict secondary structure compositional features such as \u03b1-helices, \u03b2-strands and coils with ([`s4pred`](https://github.com/psipred/s4pred))\n4. Present QC stats for input sequences before and after initial pre-processing with ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nid,fasta\nspecies1,species1_proteins.fasta\nspecies2,species2_proteins.fasta\n```\n\nEach row represents a FASTA file of proteins from a single species.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/proteinannotator \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/proteinannotator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/proteinannotator/output).\n\n## Credits\n\nnf-core/proteinannotator was originally written by Olga Botvinnik and Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Michael L Heuer](https://github.com/heuermh)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Eric Wei](https://github.com/eweizy)\n- [Martin Beracochea](https://github.com/mberacochea)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.18547735](https://doi.org/10.5281/zenodo.18547735)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "description": "

\n \n \n \"nf-core/proteinannotator\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/proteinannotator)\n[![GitHub Actions CI Status](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.18547735-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.18547735)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinannotator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23proteinannotator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/proteinannotator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/proteinannotator** is a bioinformatics pipeline that computes statistics for protein FASTA inputs and produces protein annotations based on predicted sequence features, including conserved domains, functions, and secondary structure.\n\n

\n \n \n \"nf-core/proteinannotator\"\n \n

\n\n### Check quality and pre-process\n\nGenerate input amino acid sequence statistics with ([`SeqFu`](https://github.com/telatin/seqfu2/)) and pre-process them (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences) with ([`SeqKit`](https://github.com/shenwei356/seqkit/))\n\n### Annotate sequences\n\n1. Conserved domain annotation with ([`hmmer`](https://github.com/EddyRivasLab/hmmer/)) against databases\n such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/), [FunFam](https://download.cathdb.info/cath/releases/all-releases/), and [NMPFams and metagRoot](https://pavlopoulos-lab.org/envofams/databases/hmmer/)\n2. Functional annotation:\n - ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.\n - ([`KOfamScan`](https://github.com/takaram/kofam_scan)) assigns KEGG Orthologs to protein sequences using profile HMMs and KO-specific score thresholds.\n3. Predict secondary structure compositional features such as \u03b1-helices, \u03b2-strands and coils with ([`s4pred`](https://github.com/psipred/s4pred))\n4. Present QC stats for input sequences before and after initial pre-processing with ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nid,fasta\nspecies1,species1_proteins.fasta\nspecies2,species2_proteins.fasta\n```\n\nEach row represents a FASTA file of proteins from a single species.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/proteinannotator \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/proteinannotator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/proteinannotator/output).\n\n## Credits\n\nnf-core/proteinannotator was originally written by Olga Botvinnik and Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Michael L Heuer](https://github.com/heuermh)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Eric Wei](https://github.com/eweizy)\n- [Martin Beracochea](https://github.com/mberacochea)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.18547735](https://doi.org/10.5281/zenodo.18547735)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" From eeab13cdfa3979c64c1d92f433d359d11adbb23a Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Wed, 2 Sep 2026 11:25:05 +0100 Subject: [PATCH 3/8] wip s update to match new template + end-to-end snapshot update --- modules.json | 12 +- modules/nf-core/seqfu/stats/meta.yml | 5 + .../nf-core/seqkit/replace/environment.yml | 2 +- modules/nf-core/seqkit/replace/main.nf | 21 ++- modules/nf-core/seqkit/replace/meta.yml | 5 + .../nf-core/seqkit/replace/tests/main.nf.test | 80 ++++----- .../seqkit/replace/tests/main.nf.test.snap | 104 +++--------- .../seqkit/replace/tests/nextflow.config | 5 + .../seqkit/replace/tests/replace.config | 5 - .../seqkit/replace/tests/uncomp.config | 6 - modules/nf-core/seqkit/rmdup/environment.yml | 2 +- modules/nf-core/seqkit/rmdup/main.nf | 52 +++--- .../nf-core/seqkit/rmdup/tests/main.nf.test | 33 ++-- .../seqkit/rmdup/tests/main.nf.test.snap | 155 +++--------------- modules/nf-core/seqkit/seq/environment.yml | 2 +- modules/nf-core/seqkit/seq/main.nf | 12 +- modules/nf-core/seqkit/seq/tests/main.nf.test | 47 +++--- .../seqkit/seq/tests/main.nf.test.snap | 92 ++--------- .../nf-core/seqkit/seq/tests/nextflow.config | 4 +- subworkflows/nf-core/faa_seqfu_seqkit/main.nf | 2 +- .../faa_seqfu_seqkit/tests/main.nf.test.snap | 12 +- .../faa_seqfu_seqkit/tests/nextflow.config | 3 - tests/default.nf.test.snap | 14 +- 23 files changed, 236 insertions(+), 439 deletions(-) create mode 100644 modules/nf-core/seqkit/replace/tests/nextflow.config delete mode 100644 modules/nf-core/seqkit/replace/tests/replace.config delete mode 100644 modules/nf-core/seqkit/replace/tests/uncomp.config diff --git a/modules.json b/modules.json index 415b0eb..4bcf981 100644 --- a/modules.json +++ b/modules.json @@ -43,22 +43,22 @@ }, "seqfu/stats": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "e0c07e2169e7569da58d8d8c3ca71023fc6a217e", "installed_by": ["faa_seqfu_seqkit"] }, "seqkit/replace": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "d07a945f421a4a91ce4e5a22db63e0e7f8741607", "installed_by": ["faa_seqfu_seqkit"] }, "seqkit/rmdup": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "d07a945f421a4a91ce4e5a22db63e0e7f8741607", "installed_by": ["faa_seqfu_seqkit"] }, "seqkit/seq": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "d07a945f421a4a91ce4e5a22db63e0e7f8741607", "installed_by": ["faa_seqfu_seqkit"] }, "untar": { @@ -72,12 +72,12 @@ "nf-core": { "faa_seqfu_seqkit": { "branch": "master", - "git_sha": "bf70cbf44b42ff4a81afcb673fcef604f5ef3a85", + "git_sha": "d07a945f421a4a91ce4e5a22db63e0e7f8741607", "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", + "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { diff --git a/modules/nf-core/seqfu/stats/meta.yml b/modules/nf-core/seqfu/stats/meta.yml index 856e6f7..a172cc5 100644 --- a/modules/nf-core/seqfu/stats/meta.yml +++ b/modules/nf-core/seqfu/stats/meta.yml @@ -12,6 +12,11 @@ tools: documentation: "https://telatin.github.io/seqfu2/" tool_dev_url: "https://github.com/telatin/seqfu2" doi: "10.3390/bioengineering8050059" + publication: + author: "Telatin A., Fariselli P. & Birolo G." + year: 2021 + title: "SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files" + source: "Bioengineering" licence: - "GPL v3" identifier: biotools:seqfu diff --git a/modules/nf-core/seqkit/replace/environment.yml b/modules/nf-core/seqkit/replace/environment.yml index b26fb1e..09abb79 100644 --- a/modules/nf-core/seqkit/replace/environment.yml +++ b/modules/nf-core/seqkit/replace/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::seqkit=2.9.0 + - bioconda::seqkit=2.13.0 diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf index 6abbd14..18a1b99 100644 --- a/modules/nf-core/seqkit/replace/main.nf +++ b/modules/nf-core/seqkit/replace/main.nf @@ -4,11 +4,12 @@ process SEQKIT_REPLACE { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' - : 'quay.io/biocontainers/seqkit:2.9.0--h9ee0642_0'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fe272ab9a519cf418160471a485b5ef50ea3f571a8e4555a826f70a4d8243ae/data' + : 'community.wave.seqera.io/library/seqkit:2.13.0--05c0a96bf9fb2751'}" input: tuple val(meta), path(fastx) + val out_ext output: tuple val(meta), path("*.fast*"), emit: fastx @@ -28,7 +29,7 @@ process SEQKIT_REPLACE { if ("${fastx}" ==~ /.+\.gz/) { isgz = ".gz" } - def endswith = task.ext.suffix ?: "${extension}${isgz}" + def endswith = out_ext ?: "${extension}${isgz}" """ seqkit \\ replace \\ @@ -39,14 +40,22 @@ process SEQKIT_REPLACE { """ stub: + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def extension = "fastq" - if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) { + if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.faa|.+\.faa.gz/) { extension = "fasta" } - def endswith = task.ext.suffix ?: "${extension}.gz" + def isgz = "" + if ("${fastx}" ==~ /.+\.gz/) { + isgz = ".gz" + } + def endswith = out_ext ?: "${extension}${isgz}" + def create_cmd = endswith.endsWith('gz') ? "echo '' | gzip >" : "touch" """ - echo "" | gzip > ${prefix}.${endswith} + echo ${args} + + ${create_cmd} ${prefix}.${endswith} """ } diff --git a/modules/nf-core/seqkit/replace/meta.yml b/modules/nf-core/seqkit/replace/meta.yml index ed1e818..e8ef679 100644 --- a/modules/nf-core/seqkit/replace/meta.yml +++ b/modules/nf-core/seqkit/replace/meta.yml @@ -27,6 +27,11 @@ input: pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" ontologies: - edam: http://edamontology.org/format_1930 # FASTQ + - out_ext: + type: string + description: > + Output file extension. Leave empty to auto-detect from input (for example + `.fasta`, `.fasta.gz`) output: fastx: - - meta: diff --git a/modules/nf-core/seqkit/replace/tests/main.nf.test b/modules/nf-core/seqkit/replace/tests/main.nf.test index 15fb7d3..679312e 100644 --- a/modules/nf-core/seqkit/replace/tests/main.nf.test +++ b/modules/nf-core/seqkit/replace/tests/main.nf.test @@ -9,97 +9,103 @@ nextflow_process { tag "seqkit" tag "seqkit/replace" - test("sarscov2 - fasta - replace") { - - config "./replace.config" + config "./nextflow.config" + test("sarscov2 - fasta - replace") { when { + params { + modules_args = "-s -p 'A' -r 'N'" + } process { """ - input[0] = [ [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta.gz', checkIfExists: true) ] - ] + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta.gz', checkIfExists: true) + ] + input[1] = '' """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } - test("sarscov2 - fasta - replace - uncompressed") { - - config "./replace.config" - when { + params { + modules_args = "-s -p 'A' -r 'N'" + } process { """ - input[0] = [ [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - ] + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = '' """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } test("sarscov2 - fasta - uncomp - custom") { - - config "./uncomp.config" - when { + params { + modules_args = "-s -p 'T' -r 'N'" + } process { """ - input[0] = [ [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - ] + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = 'fasta' """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } test("sarscov2 - fasta - stub") { - - options "-stub" + options '-stub' when { + params { + modules_args = "" + } process { """ - input[0] = [ [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - ] + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = '' """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } - } diff --git a/modules/nf-core/seqkit/replace/tests/main.nf.test.snap b/modules/nf-core/seqkit/replace/tests/main.nf.test.snap index fdae3eb..02bace1 100644 --- a/modules/nf-core/seqkit/replace/tests/main.nf.test.snap +++ b/modules/nf-core/seqkit/replace/tests/main.nf.test.snap @@ -2,62 +2,32 @@ "sarscov2 - fasta - stub": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - [ - "SEQKIT_REPLACE", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { "id": "test" }, - "test.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_seqkit": [ [ "SEQKIT_REPLACE", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], + "timestamp": "2026-06-13T12:47:21.226842064", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T14:51:31.369966565" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, "sarscov2 - fasta - replace - uncompressed": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.fasta:md5,b1518908253a4997fcad98270751112e" - ] - ], - "1": [ - [ - "SEQKIT_REPLACE", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { @@ -70,76 +40,46 @@ [ "SEQKIT_REPLACE", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], + "timestamp": "2026-06-12T17:26:01.449665395", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T14:51:20.851601162" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, "sarscov2 - fasta - uncomp - custom": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test..fasta:md5,05d3294a62c72f5489f067c1da3c2f6c" - ] - ], - "1": [ - [ - "SEQKIT_REPLACE", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { "id": "test" }, - "test..fasta:md5,05d3294a62c72f5489f067c1da3c2f6c" + "test.fasta:md5,05d3294a62c72f5489f067c1da3c2f6c" ] ], "versions_seqkit": [ [ "SEQKIT_REPLACE", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], + "timestamp": "2026-06-13T12:54:19.323281146", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T14:51:26.121667583" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, "sarscov2 - fasta - replace": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.fasta.gz:md5,c40eaff961f6f2a48bb7e8fd156ed5d7" - ] - ], - "1": [ - [ - "SEQKIT_REPLACE", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { @@ -152,15 +92,15 @@ [ "SEQKIT_REPLACE", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], + "timestamp": "2026-06-12T17:25:54.471016576", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-03T14:51:15.520168225" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } } } \ No newline at end of file diff --git a/modules/nf-core/seqkit/replace/tests/nextflow.config b/modules/nf-core/seqkit/replace/tests/nextflow.config new file mode 100644 index 0000000..09856f3 --- /dev/null +++ b/modules/nf-core/seqkit/replace/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: SEQKIT_REPLACE { + ext.args = params.modules_args ?: '' + } +} diff --git a/modules/nf-core/seqkit/replace/tests/replace.config b/modules/nf-core/seqkit/replace/tests/replace.config deleted file mode 100644 index 8766447..0000000 --- a/modules/nf-core/seqkit/replace/tests/replace.config +++ /dev/null @@ -1,5 +0,0 @@ - process { - withName: 'SEQKIT_REPLACE' { - ext.args = "-s -p 'A' -r 'N'" - } - } diff --git a/modules/nf-core/seqkit/replace/tests/uncomp.config b/modules/nf-core/seqkit/replace/tests/uncomp.config deleted file mode 100644 index dbd892b..0000000 --- a/modules/nf-core/seqkit/replace/tests/uncomp.config +++ /dev/null @@ -1,6 +0,0 @@ - process { - withName: 'SEQKIT_REPLACE' { - ext.args = "-s -p 'T' -r 'N'" - ext.suffix = ".fasta" - } - } diff --git a/modules/nf-core/seqkit/rmdup/environment.yml b/modules/nf-core/seqkit/rmdup/environment.yml index b26fb1e..09abb79 100644 --- a/modules/nf-core/seqkit/rmdup/environment.yml +++ b/modules/nf-core/seqkit/rmdup/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::seqkit=2.9.0 + - bioconda::seqkit=2.13.0 diff --git a/modules/nf-core/seqkit/rmdup/main.nf b/modules/nf-core/seqkit/rmdup/main.nf index 22f3b1a..7f86538 100644 --- a/modules/nf-core/seqkit/rmdup/main.nf +++ b/modules/nf-core/seqkit/rmdup/main.nf @@ -1,54 +1,62 @@ process SEQKIT_RMDUP { - tag "$meta.id" + tag "${meta.id}" label 'process_low' // File IO can be a bottleneck. See: https://bioinf.shenwei.me/seqkit/usage/#parallelization-of-cpu-intensive-jobs conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0': - 'quay.io/biocontainers/seqkit:2.9.0--h9ee0642_0' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fe272ab9a519cf418160471a485b5ef50ea3f571a8e4555a826f70a4d8243ae/data' + : 'community.wave.seqera.io/library/seqkit:2.13.0--05c0a96bf9fb2751'}" input: tuple val(meta), path(fastx) output: - tuple val(meta), path("${prefix}.${extension}") , emit: fastx - tuple val(meta), path("*.log") , emit: log + tuple val(meta), path("${prefix}.${extension}"), emit: fastx + tuple val(meta), path("*.log"), emit: log tuple val("${task.process}"), val('seqkit'), eval("seqkit version | sed 's/^.*v//'"), emit: versions_seqkit, topic: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - extension = "fastq" - if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) { - extension = "fasta" + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + extension = "fastq" + if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) { + extension = "fasta" } - extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension + extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension // SeqKit/rmdup takes care of compressing the output: https://bioinf.shenwei.me/seqkit/usage/#rmdup - if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + if ("${prefix}.${extension}" == "${fastx}") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } """ seqkit \\ rmdup \\ - --threads $task.cpus \\ - $args \\ - $fastx \\ + --threads ${task.cpus} \\ + ${args} \\ + ${fastx} \\ -o ${prefix}.${extension} \\ 2>| >(tee ${prefix}.log >&2) """ stub: - prefix = task.ext.prefix ?: "${meta.id}" - extension = "fastq" - if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) { - extension = "fasta" + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + extension = "fastq" + if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) { + extension = "fasta" } extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension - if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + if ("${prefix}.${extension}" == "${fastx}") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } + def create_cmd = extension.endsWith('gz') ? "echo '' | gzip >" : "touch" """ - touch ${prefix}.${extension} + echo ${args} + + ${create_cmd} ${prefix}.${extension} echo \\ '[INFO] 0 duplicated records removed' \\ > ${prefix}.log diff --git a/modules/nf-core/seqkit/rmdup/tests/main.nf.test b/modules/nf-core/seqkit/rmdup/tests/main.nf.test index beac3a4..411a2dd 100644 --- a/modules/nf-core/seqkit/rmdup/tests/main.nf.test +++ b/modules/nf-core/seqkit/rmdup/tests/main.nf.test @@ -22,13 +22,12 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(sanitizeOutput(process.out)).match() }, { assert path(process.out.log[0][1]).text.contains('0 duplicated records removed') } ) } - } test("repeated-fasta") { @@ -47,13 +46,12 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(sanitizeOutput(process.out)).match() }, { assert path(process.out.log[0][1]).text.contains('1 duplicated records removed') } ) } - } test("sarscov2-genome_fasta_gz") { @@ -69,13 +67,12 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(sanitizeOutput(process.out)).match() }, { assert path(process.out.log[0][1]).text.contains('0 duplicated records removed') } ) } - } test("sarscov2-test_1_fastq_gz") { @@ -91,13 +88,12 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(sanitizeOutput(process.out)).match() }, { assert path(process.out.log[0][1]).text.contains('0 duplicated records removed') } ) } - } test("file_name_conflict-fail_with_error") { @@ -113,16 +109,14 @@ nextflow_process { } then { + assert process.failed assertAll( - { assert !process.success }, { assert process.stdout.toString().contains("Input and output names are the same") } ) } - } test("sarscov2-genome_fasta-stub") { - options '-stub' when { @@ -137,13 +131,12 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(sanitizeOutput(process.out)).match() }, { assert path(process.out.log[0][1]).text.contains('0 duplicated records removed') } ) } - } test("file_name_conflict-fail_with_error-stub") { @@ -161,12 +154,10 @@ nextflow_process { } then { + assert process.failed assertAll( - { assert !process.success }, { assert process.stdout.toString().contains("Input and output names are the same") } ) } - } - } diff --git a/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap b/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap index 764cd09..0bd79b3 100644 --- a/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap +++ b/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap @@ -2,29 +2,6 @@ "sarscov2-genome_fasta-stub": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.log:md5,cf833211befdf890bb6b2a3cd0b91853" - ] - ], - "2": [ - [ - "SEQKIT_RMDUP", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { @@ -45,43 +22,20 @@ [ "SEQKIT_RMDUP", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], - "timestamp": "2026-03-12T13:08:29.041177508", + "timestamp": "2026-06-12T17:26:48.435786445", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "sarscov2-test_1_fastq_gz": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.log:md5,a41135cfe024baaf42f135583fe73f0d" - ] - ], - "2": [ - [ - "SEQKIT_RMDUP", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { @@ -102,43 +56,20 @@ [ "SEQKIT_RMDUP", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], - "timestamp": "2026-03-12T13:08:15.046237092", + "timestamp": "2026-06-12T17:26:39.040489053", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "sarscov2-genome_fasta": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.fasta:md5,483f4a5dfe60171c86ee9b7e6dff908b" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.log:md5,a41135cfe024baaf42f135583fe73f0d" - ] - ], - "2": [ - [ - "SEQKIT_RMDUP", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { @@ -159,43 +90,20 @@ [ "SEQKIT_RMDUP", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], - "timestamp": "2026-03-12T13:07:53.771340434", + "timestamp": "2026-06-12T17:26:21.035761383", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "repeated-fasta": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.fasta:md5,7510a742291241e7d7556bf720caf65c" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.log:md5,314c0aaef0f832a217a3f6ce3f8bc117" - ] - ], - "2": [ - [ - "SEQKIT_RMDUP", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { @@ -216,43 +124,20 @@ [ "SEQKIT_RMDUP", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], - "timestamp": "2026-03-12T13:08:00.578741348", + "timestamp": "2026-06-12T17:26:26.868734329", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "sarscov2-genome_fasta_gz": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.fasta.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.log:md5,a41135cfe024baaf42f135583fe73f0d" - ] - ], - "2": [ - [ - "SEQKIT_RMDUP", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { @@ -273,15 +158,15 @@ [ "SEQKIT_RMDUP", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], - "timestamp": "2026-03-12T13:08:07.836784907", + "timestamp": "2026-06-12T17:26:33.522032009", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/modules/nf-core/seqkit/seq/environment.yml b/modules/nf-core/seqkit/seq/environment.yml index b26fb1e..09abb79 100644 --- a/modules/nf-core/seqkit/seq/environment.yml +++ b/modules/nf-core/seqkit/seq/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::seqkit=2.9.0 + - bioconda::seqkit=2.13.0 diff --git a/modules/nf-core/seqkit/seq/main.nf b/modules/nf-core/seqkit/seq/main.nf index d78040a..3bade4e 100644 --- a/modules/nf-core/seqkit/seq/main.nf +++ b/modules/nf-core/seqkit/seq/main.nf @@ -5,8 +5,8 @@ process SEQKIT_SEQ { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' - : 'quay.io/biocontainers/seqkit:2.9.0--h9ee0642_0'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fe272ab9a519cf418160471a485b5ef50ea3f571a8e4555a826f70a4d8243ae/data' + : 'community.wave.seqera.io/library/seqkit:2.13.0--05c0a96bf9fb2751'}" input: tuple val(meta), path(fastx) @@ -42,6 +42,8 @@ process SEQKIT_SEQ { """ stub: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' prefix = task.ext.prefix ?: "${meta.id}" def extension = "fastq" if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) { @@ -51,7 +53,11 @@ process SEQKIT_SEQ { if ("${prefix}.${extension}" == "${fastx}") { error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") } + def create_cmd = extension.endsWith('gz') ? "echo '' | gzip >" : "touch" """ - touch ${prefix}.${extension} + echo ${args} + echo ${args2} + + ${create_cmd} ${prefix}.${extension} """ } diff --git a/modules/nf-core/seqkit/seq/tests/main.nf.test b/modules/nf-core/seqkit/seq/tests/main.nf.test index 9fd1c08..457be88 100644 --- a/modules/nf-core/seqkit/seq/tests/main.nf.test +++ b/modules/nf-core/seqkit/seq/tests/main.nf.test @@ -12,6 +12,9 @@ nextflow_process { test("sarscov2-genome_fasta") { when { + params { + modules_args2 = '-n' + } process { """ input[0] = [ @@ -23,16 +26,18 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } test("sarscov2-genome_fasta_gz") { when { + params { + modules_args2 = '-n' + } process { """ input[0] = [ @@ -44,16 +49,18 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } test("sarscov2-test_1_fastq_gz") { when { + params { + modules_args2 = '-n' + } process { """ input[0] = [ @@ -65,16 +72,18 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } test("file_name_conflict-fail_with_error") { when { + params { + modules_args2 = '-n' + } process { """ input[0] = [ @@ -86,19 +95,20 @@ nextflow_process { } then { + assert process.failed assertAll( - { assert !process.success }, { assert process.stdout.toString().contains("Input and output names are the same") } ) } - } test("sarscov2-genome_fasta-stub") { - options '-stub' when { + params { + modules_args2 = '-n' + } process { """ input[0] = [ @@ -110,19 +120,20 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } test("file_name_conflict-fail_with_error-stub") { - options '-stub' when { + params { + modules_args2 = '-n' + } process { """ input[0] = [ @@ -134,12 +145,10 @@ nextflow_process { } then { + assert process.failed assertAll( - { assert !process.success }, { assert process.stdout.toString().contains("Input and output names are the same") } ) } - } - } diff --git a/modules/nf-core/seqkit/seq/tests/main.nf.test.snap b/modules/nf-core/seqkit/seq/tests/main.nf.test.snap index bbcc995..d8e79f6 100644 --- a/modules/nf-core/seqkit/seq/tests/main.nf.test.snap +++ b/modules/nf-core/seqkit/seq/tests/main.nf.test.snap @@ -2,21 +2,6 @@ "sarscov2-genome_fasta-stub": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - "SEQKIT_SEQ", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { @@ -29,35 +14,20 @@ [ "SEQKIT_SEQ", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], - "timestamp": "2026-03-12T13:09:25.839048434", + "timestamp": "2026-06-14T18:54:38.462339108", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "sarscov2-test_1_fastq_gz": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" - ] - ], - "1": [ - [ - "SEQKIT_SEQ", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { @@ -70,35 +40,20 @@ [ "SEQKIT_SEQ", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], - "timestamp": "2026-03-12T13:09:12.72324007", + "timestamp": "2026-06-12T17:27:53.391265296", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "sarscov2-genome_fasta": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.fasta:md5,483f4a5dfe60171c86ee9b7e6dff908b" - ] - ], - "1": [ - [ - "SEQKIT_SEQ", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { @@ -111,35 +66,20 @@ [ "SEQKIT_SEQ", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], - "timestamp": "2026-03-12T13:08:58.152442646", + "timestamp": "2026-06-12T17:27:43.147566645", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "sarscov2-genome_fasta_gz": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.fasta.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b" - ] - ], - "1": [ - [ - "SEQKIT_SEQ", - "seqkit", - "2.9.0" - ] - ], "fastx": [ [ { @@ -152,15 +92,15 @@ [ "SEQKIT_SEQ", "seqkit", - "2.9.0" + "2.13.0" ] ] } ], - "timestamp": "2026-03-12T13:09:05.344232955", + "timestamp": "2026-06-12T17:27:48.241605452", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/modules/nf-core/seqkit/seq/tests/nextflow.config b/modules/nf-core/seqkit/seq/tests/nextflow.config index d8e3c66..cd1f022 100644 --- a/modules/nf-core/seqkit/seq/tests/nextflow.config +++ b/modules/nf-core/seqkit/seq/tests/nextflow.config @@ -1,3 +1,5 @@ process { - ext.args2 = '-n' + withName: SEQKIT_SEQ { + ext.args2 = params.modules_args2 ?: '' + } } diff --git a/subworkflows/nf-core/faa_seqfu_seqkit/main.nf b/subworkflows/nf-core/faa_seqfu_seqkit/main.nf index bd5b177..9a7ea77 100644 --- a/subworkflows/nf-core/faa_seqfu_seqkit/main.nf +++ b/subworkflows/nf-core/faa_seqfu_seqkit/main.nf @@ -18,7 +18,7 @@ workflow FAA_SEQFU_SEQKIT { if (!skip_preprocessing) { SEQKIT_SEQ(ch_fasta) - SEQKIT_REPLACE(SEQKIT_SEQ.out.fastx) + SEQKIT_REPLACE(SEQKIT_SEQ.out.fastx, 'fasta') SEQKIT_RMDUP(SEQKIT_REPLACE.out.fastx) ch_fasta = SEQKIT_RMDUP.out.fastx diff --git a/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap b/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap index c09fb56..e39656c 100644 --- a/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap +++ b/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap @@ -26,10 +26,10 @@ ] } ], - "timestamp": "2026-03-12T14:44:03.010426069", + "timestamp": "2026-06-13T14:16:45.234475759", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "faa": { @@ -59,10 +59,10 @@ ] } ], - "timestamp": "2026-03-12T14:43:53.509896933", + "timestamp": "2026-06-13T14:16:37.15518591", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/subworkflows/nf-core/faa_seqfu_seqkit/tests/nextflow.config b/subworkflows/nf-core/faa_seqfu_seqkit/tests/nextflow.config index 38af0eb..b0e7247 100644 --- a/subworkflows/nf-core/faa_seqfu_seqkit/tests/nextflow.config +++ b/subworkflows/nf-core/faa_seqfu_seqkit/tests/nextflow.config @@ -1,5 +1,4 @@ process { - withName: SEQFU_STATS_BEFORE { ext.prefix = { "${meta.id}_before" } } @@ -21,8 +20,6 @@ process { withName: SEQKIT_REPLACE { ext.args = '-p "/" -r "_"' - ext.suffix = "fasta" ext.prefix = "intermediate_seqkit_replace" } - } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 724f8cc..3e4f17a 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -55,13 +55,13 @@ "seqfu": "1.22.3" }, "SEQKIT_REPLACE": { - "seqkit": "2.9.0" + "seqkit": "2.13.0" }, "SEQKIT_RMDUP": { - "seqkit": "2.9.0" + "seqkit": "2.13.0" }, "SEQKIT_SEQ": { - "seqkit": "2.9.0" + "seqkit": "2.13.0" }, "UNTAR_INTERPROSCAN": { "untar": 1.34 @@ -451,10 +451,10 @@ "GI|225038609|EFDID|719595|FULL.ss2:md5,e7d8eaa84d46a6a714ffe00d7f21cdfb" ] ], - "timestamp": "2026-07-27T13:43:53.452281", + "timestamp": "2026-09-02T11:22:22.960095437", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } } -} +} \ No newline at end of file From 5462237b60810deb6d493215aee6e4a500931fa8 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Wed, 2 Sep 2026 11:28:17 +0100 Subject: [PATCH 4/8] changelog update --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2ca554c..47d684c 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). -## v1.2.0dev - [unreleased] +## v1.2.0dev - [unreleased] ### `Added` @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- [#111](https://github.com/nf-core/proteinannotator/pull/111) - nf-core tools template update to 4.1.0. (by @vagkaratzas) - [#106](https://github.com/nf-core/proteinannotator/pull/106) - nf-core tools template update to 4.0.3. (by @vagkaratzas) ## v1.1.0 - [2026/05/07] From c9e4aead2e247f23fe9146440de2d2c0c5d4a0c9 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Wed, 2 Sep 2026 11:31:05 +0100 Subject: [PATCH 5/8] seqkit v bump on changelog --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 47d684c..607c7a6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#111](https://github.com/nf-core/proteinannotator/pull/111) - nf-core tools template update to 4.1.0. (by @vagkaratzas) - [#106](https://github.com/nf-core/proteinannotator/pull/106) - nf-core tools template update to 4.0.3. (by @vagkaratzas) +### `Dependencies` + +| Tool | Previous version | New version | +| ------- | ---------------- | ----------- | +| seqkit | 2.9.0 | 2.13.0 | + ## v1.1.0 - [2026/05/07] ### `Added` From 5ed12ad72585981c84c1e3a0a32753feec52d2e7 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Wed, 2 Sep 2026 11:33:23 +0100 Subject: [PATCH 6/8] prettier fix --- CHANGELOG.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 607c7a6..7b1633f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,9 +16,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Dependencies` -| Tool | Previous version | New version | -| ------- | ---------------- | ----------- | -| seqkit | 2.9.0 | 2.13.0 | +| Tool | Previous version | New version | +| ------ | ---------------- | ----------- | +| seqkit | 2.9.0 | 2.13.0 | ## v1.1.0 - [2026/05/07] From 9853737d727e4e450194bf9fb733f862b085a9ac Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Wed, 2 Sep 2026 11:47:22 +0100 Subject: [PATCH 7/8] remove merge leftover from nf-schema subworkflow --- subworkflows/nf-core/utils_nfschema_plugin/main.nf | 3 --- 1 file changed, 3 deletions(-) diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index 9762571..9ff0681 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -69,9 +69,6 @@ workflow UTILS_NFSCHEMA_PLUGIN { if(cli_typecast != null) { validateOptions << [cast_cli_params: cli_typecast] } - if(cli_typecast != null) { - validateOptions << [cliTypecast: cli_typecast] - } validateParameters(validateOptions) } From 12d89baadc041eb344005374bbdbd0255359bfc5 Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Wed, 2 Sep 2026 13:21:48 +0100 Subject: [PATCH 8/8] remove stale conda lock files from multiqc --- .../linux_amd64-bd-c1f4a7982b743963_1.txt | 1552 ----------------- .../linux_amd64-bd-db7c73dae76bc9e6_1.txt | 126 -- .../linux_arm64-bd-40bf3b435e89dc22_1.txt | 1502 ---------------- .../linux_arm64-bd-d167b8012595a136_1.txt | 125 -- 4 files changed, 3305 deletions(-) delete mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt delete mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt delete mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt delete mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt deleted file mode 100644 index 7619030..0000000 --- a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt +++ /dev/null @@ -1,1552 +0,0 @@ - -version: 6 -environments: -default: -channels: -- url: https://conda.anaconda.org/conda-forge/ -- 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a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt +++ /dev/null @@ -1,125 +0,0 @@ - -# This file may be used to create an environment using: -# $ conda create --name --file -# platform: linux-aarch64 -@EXPLICIT -https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_18.conda#4faa39bf919939602e594253bd673958 -https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda#468fd3bb9e1f671d36c2cbc677e56f1d -https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda#552567ea2b61e3a3035759b2fdb3f9a6 -https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_9.conda#840d8fc0d7b3209be93080bc20e07f2d -https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_2.conda#502006882cf5461adced436e410046d1 -https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda#c3655f82dcea2aa179b291e7099c1fcc 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