From f7bdaeb48b1c22f0737d8a26d8c131d5b973e226 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 20 Dec 2024 16:12:19 +0000 Subject: [PATCH 01/11] major change to run CI on dev using dev conf --- .github/workflows/ci.yml | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2876c789..7e98c51c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -4,6 +4,7 @@ on: push: branches: - dev + - master pull_request: release: types: [published] @@ -28,7 +29,7 @@ jobs: name: Run pipeline with test data # Only run on push if this is the nf-core dev branch (merged PRs) - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/quantms') }} + if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'bigbio/quantms') }} runs-on: ubuntu-latest strategy: fail-fast: false @@ -50,8 +51,10 @@ jobs: include: - test_profile: test_lfq exec_profile: "conda" + condition: ${{ github.base_ref != 'dev' }} - test_profile: test_dda_id exec_profile: "conda" + condition: ${{ github.base_ref != 'dev' }} steps: - name: Check out pipeline code uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 @@ -79,7 +82,7 @@ jobs: - name: Install micromamba env: MAMBA_ROOT_PREFIX: ${{ github.workspace }}/.micromamba - if: matrix.exec_profile == 'conda' + if: matrix.exec_profile == 'conda' && github.base_ref != 'dev' run: | wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba echo "$(pwd)/bin" >> $GITHUB_PATH @@ -94,18 +97,23 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data in docker/singularity profile - if: matrix.exec_profile == 'docker' || matrix.exec_profile == 'singularity' + - name: Run pipeline with test data in docker/singularity profile (dev branch) + if: github.base_ref == 'dev' && (matrix.exec_profile == 'docker' || matrix.exec_profile == 'singularity') # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix + run: | + nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE,dev --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results + + - name: Run pipeline with test data (master/other branches) + if: github.base_ref != 'dev' && (matrix.exec_profile == 'docker' || matrix.exec_profile == 'singularity') run: | nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results - name: Run pipeline with test data in conda profile (and single-threaded) env: MAMBA_ROOT_PREFIX: ${{ github.workspace }}/.micromamba - if: matrix.exec_profile == 'conda' + if: matrix.exec_profile == 'conda' && github.base_ref != 'dev' # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix From d7d4b74d8ee56388a7cd39ad37aef4963cdf28b5 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 20 Dec 2024 16:31:58 +0000 Subject: [PATCH 02/11] Template update for nf-core/tools version 3.1.0 --- .github/CONTRIBUTING.md | 20 ++++++------- .github/ISSUE_TEMPLATE/bug_report.yml | 4 +-- .github/ISSUE_TEMPLATE/config.yml | 2 +- .github/ISSUE_TEMPLATE/feature_request.yml | 2 +- .github/PULL_REQUEST_TEMPLATE.md | 10 +++---- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awstest.yml | 2 +- .github/workflows/branch.yml | 4 +-- .github/workflows/ci.yml | 2 +- .github/workflows/fix-linting.yml | 4 +-- .nf-core.yml | 2 +- CHANGELOG.md | 4 +-- CITATIONS.md | 2 +- README.md | 18 ++++++------ assets/adaptivecard.json | 2 +- assets/email_template.html | 14 +++++----- assets/email_template.txt | 10 +++---- assets/methods_description_template.yml | 8 +++--- assets/multiqc_config.yml | 6 ++-- assets/schema_input.json | 4 +-- assets/sendmail_template.txt | 6 ++-- assets/slackreport.json | 2 +- conf/base.config | 2 +- conf/test.config | 2 +- conf/test_full.config | 2 +- docs/README.md | 4 +-- docs/output.md | 2 +- docs/usage.md | 10 +++---- main.nf | 10 +++---- modules.json | 4 +-- nextflow.config | 14 +++++----- nextflow_schema.json | 4 +-- ro-crate-metadata.json | 28 +++++++++---------- .../utils_nfcore_quantms_pipeline/main.nf | 2 +- 34 files changed, 107 insertions(+), 107 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index c2652c59..1faafd6f 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,23 +1,23 @@ -# `nf-core/quantms`: Contributing Guidelines +# `bigbio/quantms`: Contributing Guidelines Hi there! -Many thanks for taking an interest in improving nf-core/quantms. +Many thanks for taking an interest in improving bigbio/quantms. -We try to manage the required tasks for nf-core/quantms using GitHub issues, you probably came to this page when creating one. +We try to manage the required tasks for bigbio/quantms using GitHub issues, you probably came to this page when creating one. Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) > [!NOTE] -> If you need help using or modifying nf-core/quantms then the best place to ask is on the nf-core Slack [#quantms](https://nfcore.slack.com/channels/quantms) channel ([join our Slack here](https://nf-co.re/join/slack)). +> If you need help using or modifying bigbio/quantms then the best place to ask is on the nf-core Slack [#quantms](https://nfcore.slack.com/channels/quantms) channel ([join our Slack here](https://nf-co.re/join/slack)). ## Contribution workflow -If you'd like to write some code for nf-core/quantms, the standard workflow is as follows: +If you'd like to write some code for bigbio/quantms, the standard workflow is as follows: -1. Check that there isn't already an issue about your idea in the [nf-core/quantms issues](https://github.com/nf-core/quantms/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/quantms repository](https://github.com/nf-core/quantms) to your GitHub account +1. Check that there isn't already an issue about your idea in the [bigbio/quantms issues](https://github.com/bigbio/quantms/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this +2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [bigbio/quantms repository](https://github.com/bigbio/quantms) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) 4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged @@ -61,11 +61,11 @@ These tests are run both with the latest available version of `Nextflow` and als ## Getting help -For further information/help, please consult the [nf-core/quantms documentation](https://nf-co.re/quantms/usage) and don't hesitate to get in touch on the nf-core Slack [#quantms](https://nfcore.slack.com/channels/quantms) channel ([join our Slack here](https://nf-co.re/join/slack)). +For further information/help, please consult the [bigbio/quantms documentation](https://nf-co.re/quantms/usage) and don't hesitate to get in touch on the nf-core Slack [#quantms](https://nfcore.slack.com/channels/quantms) channel ([join our Slack here](https://nf-co.re/join/slack)). ## Pipeline contribution conventions -To make the `nf-core/quantms` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. +To make the `bigbio/quantms` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. ### Adding a new step @@ -115,7 +115,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes To get started: -- Open the repo in [Codespaces](https://github.com/nf-core/quantms/codespaces) +- Open the repo in [Codespaces](https://github.com/bigbio/quantms/codespaces) - Tools installed - nf-core - Nextflow diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 5d2a613d..48f4ce30 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -8,7 +8,7 @@ body: Before you post this issue, please check the documentation: - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - - [nf-core/quantms pipeline documentation](https://nf-co.re/quantms/usage) + - [bigbio/quantms pipeline documentation](https://nf-co.re/quantms/usage) - type: textarea id: description @@ -47,4 +47,4 @@ body: * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ - * Version of nf-core/quantms _(eg. 1.1, 1.5, 1.8.2)_ + * Version of bigbio/quantms _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index d95f2b96..9e75d2ca 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -4,4 +4,4 @@ contact_links: about: Please join the nf-core community here - name: "Slack #quantms channel" url: https://nfcore.slack.com/channels/quantms - about: Discussion about the nf-core/quantms pipeline + about: Discussion about the bigbio/quantms pipeline diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml index bf4a3f9d..b99a1dbf 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.yml +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -1,5 +1,5 @@ name: Feature request -description: Suggest an idea for the nf-core/quantms pipeline +description: Suggest an idea for the bigbio/quantms pipeline labels: enhancement body: - type: textarea diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 195e7b5e..32eca5fd 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,22 +1,22 @@ ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/quantms/tree/master/.github/CONTRIBUTING.md) -- [ ] If necessary, also make a PR on the nf-core/quantms _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/bigbio/quantms/tree/master/.github/CONTRIBUTING.md) +- [ ] If necessary, also make a PR on the bigbio/quantms _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index ffb42a60..42cefd77 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -16,7 +16,7 @@ jobs: run-platform: name: Run AWS full tests # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered - if: github.repository == 'nf-core/quantms' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' + if: github.repository == 'bigbio/quantms' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest steps: - name: Get PR reviews diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index fc6b10f7..769feb09 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -7,7 +7,7 @@ on: jobs: run-platform: name: Run AWS tests - if: github.repository == 'nf-core/quantms' + if: github.repository == 'bigbio/quantms' runs-on: ubuntu-latest steps: # Launch workflow using Seqera Platform CLI tool action diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index cab98632..3743d71a 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -13,9 +13,9 @@ jobs: steps: # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - name: Check PRs - if: github.repository == 'nf-core/quantms' + if: github.repository == 'bigbio/quantms' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/quantms ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ ${{github.event.pull_request.head.repo.full_name }} == bigbio/quantms ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6bb23ebc..6d00f668 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -22,7 +22,7 @@ jobs: test: name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/quantms') }}" + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'bigbio/quantms') }}" runs-on: ubuntu-latest strategy: matrix: diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 821148fc..aeb9fcb3 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -9,7 +9,7 @@ jobs: if: > contains(github.event.comment.html_url, '/pull/') && contains(github.event.comment.body, '@nf-core-bot fix linting') && - github.repository == 'nf-core/quantms' + github.repository == 'bigbio/quantms' runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later @@ -86,4 +86,4 @@ jobs: issue-number: ${{ github.event.issue.number }} body: | @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. - See [CI log](https://github.com/nf-core/quantms/actions/runs/${{ github.run_id }}) for more details. + See [CI log](https://github.com/bigbio/quantms/actions/runs/${{ github.run_id }}) for more details. diff --git a/.nf-core.yml b/.nf-core.yml index 43c3a2ba..d6cb9511 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -21,6 +21,6 @@ template: force: false is_nfcore: true name: quantms - org: nf-core + org: bigbio outdir: . version: 1.3.1dev diff --git a/CHANGELOG.md b/CHANGELOG.md index 8a83258a..89b54605 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,11 +1,11 @@ -# nf-core/quantms: Changelog +# bigbio/quantms: Changelog 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). ## v1.3.1dev - [date] -Initial release of nf-core/quantms, created with the [nf-core](https://nf-co.re/) template. +Initial release of bigbio/quantms, created with the [nf-core](https://nf-co.re/) template. ### `Added` diff --git a/CITATIONS.md b/CITATIONS.md index f98356d1..8cf8ea3c 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -1,4 +1,4 @@ -# nf-core/quantms: Citations +# bigbio/quantms: Citations ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) diff --git a/README.md b/README.md index 880a187c..2411c623 100644 --- a/README.md +++ b/README.md @@ -1,25 +1,25 @@

- - nf-core/quantms + + bigbio/quantms

-[![GitHub Actions CI Status](https://github.com/nf-core/quantms/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/quantms/actions/workflows/ci.yml) -[![GitHub Actions Linting Status](https://github.com/nf-core/quantms/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/quantms/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/quantms/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions CI Status](https://github.com/bigbio/quantms/actions/workflows/ci.yml/badge.svg)](https://github.com/bigbio/quantms/actions/workflows/ci.yml) +[![GitHub Actions Linting Status](https://github.com/bigbio/quantms/actions/workflows/linting.yml/badge.svg)](https://github.com/bigbio/quantms/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/quantms/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) [![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/) -[![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/quantms) +[![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/bigbio/quantms) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23quantms-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/quantms)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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) ## Introduction -**nf-core/quantms** is a bioinformatics pipeline that ... +**bigbio/quantms** is a bioinformatics pipeline that ... ```bash -nextflow run nf-core/quantms \ +nextflow run bigbio/quantms \ -profile \ --input samplesheet.csv \ --outdir @@ -79,7 +79,7 @@ For more details about the output files and reports, please refer to the ## Credits -nf-core/quantms was originally written by Yasset Perez-Riverol. +bigbio/quantms was originally written by Yasset Perez-Riverol. We thank the following people for their extensive assistance in the development of this pipeline: @@ -94,7 +94,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations - + diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json index 5af06e53..4aba45f1 100644 --- a/assets/adaptivecard.json +++ b/assets/adaptivecard.json @@ -17,7 +17,7 @@ "size": "Large", "weight": "Bolder", "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", - "text": "nf-core/quantms v${version} - ${runName}", + "text": "bigbio/quantms v${version} - ${runName}", "wrap": true }, { diff --git a/assets/email_template.html b/assets/email_template.html index 9010ff46..ebc0ee06 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -4,21 +4,21 @@ - - nf-core/quantms Pipeline Report + + bigbio/quantms Pipeline Report
-

nf-core/quantms ${version}

+

bigbio/quantms ${version}

Run Name: $runName

<% if (!success){ out << """
-

nf-core/quantms execution completed unsuccessfully!

+

bigbio/quantms execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: $exitStatus.

The full error message was:

${errorReport}
@@ -27,7 +27,7 @@

nf-core/quantms execution completed un } else { out << """
- nf-core/quantms execution completed successfully! + bigbio/quantms execution completed successfully!
""" } @@ -44,8 +44,8 @@

Pipeline Configuration:

-

nf-core/quantms

-

https://github.com/nf-core/quantms

+

bigbio/quantms

+

https://github.com/bigbio/quantms

diff --git a/assets/email_template.txt b/assets/email_template.txt index da8858d2..451dfacb 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -4,15 +4,15 @@ |\\ | |__ __ / ` / \\ |__) |__ } { | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-, `._,._,' - nf-core/quantms ${version} + bigbio/quantms ${version} ---------------------------------------------------- Run Name: $runName <% if (success){ - out << "## nf-core/quantms execution completed successfully! ##" + out << "## bigbio/quantms execution completed successfully! ##" } else { out << """#################################################### -## nf-core/quantms execution completed unsuccessfully! ## +## bigbio/quantms execution completed unsuccessfully! ## #################################################### The exit status of the task that caused the workflow execution to fail was: $exitStatus. The full error message was: @@ -35,5 +35,5 @@ Pipeline Configuration: <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %> -- -nf-core/quantms -https://github.com/nf-core/quantms +bigbio/quantms +https://github.com/bigbio/quantms diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 54ba5052..70ee8b50 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -1,13 +1,13 @@ -id: "nf-core-quantms-methods-description" +id: "bigbio-quantms-methods-description" description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." -section_name: "nf-core/quantms Methods Description" -section_href: "https://github.com/nf-core/quantms" +section_name: "bigbio/quantms Methods Description" +section_href: "https://github.com/bigbio/quantms" plot_type: "html" ## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

Data was processed using nf-core/quantms v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

+

Data was processed using bigbio/quantms v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}

${tool_citations}

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d9503f5b..6a080791 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,13 +1,13 @@ report_comment: > - This report has been generated by the nf-core/quantms + This report has been generated by the bigbio/quantms analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: - "nf-core-quantms-methods-description": + "bigbio-quantms-methods-description": order: -1000 software_versions: order: -1001 - "nf-core-quantms-summary": + "bigbio-quantms-summary": order: -1002 export_plots: true diff --git a/assets/schema_input.json b/assets/schema_input.json index b3fe9935..789941d0 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/quantms/master/assets/schema_input.json", - "title": "nf-core/quantms pipeline - params.input schema", + "$id": "https://raw.githubusercontent.com/bigbio/quantms/master/assets/schema_input.json", + "title": "bigbio/quantms pipeline - params.input schema", "description": "Schema for the file provided with params.input", "type": "array", "items": { diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt index e0abebee..7142438d 100644 --- a/assets/sendmail_template.txt +++ b/assets/sendmail_template.txt @@ -9,12 +9,12 @@ Content-Type: text/html; charset=utf-8 $email_html --nfcoremimeboundary -Content-Type: image/png;name="nf-core-quantms_logo.png" +Content-Type: image/png;name="bigbio-quantms_logo.png" Content-Transfer-Encoding: base64 Content-ID: -Content-Disposition: inline; filename="nf-core-quantms_logo_light.png" +Content-Disposition: inline; filename="bigbio-quantms_logo_light.png" -<% out << new File("$projectDir/assets/nf-core-quantms_logo_light.png"). +<% out << new File("$projectDir/assets/bigbio-quantms_logo_light.png"). bytes. encodeBase64(). toString(). diff --git a/assets/slackreport.json b/assets/slackreport.json index 34ac0761..487dd560 100644 --- a/assets/slackreport.json +++ b/assets/slackreport.json @@ -3,7 +3,7 @@ { "fallback": "Plain-text summary of the attachment.", "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "nf-core/quantms ${version} - ${runName}", + "author_name": "bigbio/quantms ${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/base.config b/conf/base.config index 5fc9d9b8..3796243a 100644 --- a/conf/base.config +++ b/conf/base.config @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - nf-core/quantms Nextflow base config file + bigbio/quantms Nextflow base config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A 'blank slate' config file, appropriate for general use on most high performance compute environments. Assumes that all software is installed and available on diff --git a/conf/test.config b/conf/test.config index 07c6cc4b..ea2f39fd 100644 --- a/conf/test.config +++ b/conf/test.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run nf-core/quantms -profile test, --outdir + nextflow run bigbio/quantms -profile test, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_full.config b/conf/test_full.config index 0a9187c2..199b7720 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run nf-core/quantms -profile test_full, --outdir + nextflow run bigbio/quantms -profile test_full, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/docs/README.md b/docs/README.md index d7a6ae3e..35a0032c 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,6 +1,6 @@ -# nf-core/quantms: Documentation +# bigbio/quantms: Documentation -The nf-core/quantms documentation is split into the following pages: +The bigbio/quantms documentation is split into the following pages: - [Usage](usage.md) - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. diff --git a/docs/output.md b/docs/output.md index 8b172c84..2de6349e 100644 --- a/docs/output.md +++ b/docs/output.md @@ -1,4 +1,4 @@ -# nf-core/quantms: Output +# bigbio/quantms: Output ## Introduction diff --git a/docs/usage.md b/docs/usage.md index 68b4ed6f..e2def00a 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -1,4 +1,4 @@ -# nf-core/quantms: Usage +# bigbio/quantms: Usage ## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/quantms/usage](https://nf-co.re/quantms/usage) @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/quantms --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker +nextflow run bigbio/quantms --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -81,7 +81,7 @@ Pipeline settings can be provided in a `yaml` or `json` file via `-params-file < The above pipeline run specified with a params file in yaml format: ```bash -nextflow run nf-core/quantms -profile docker -params-file params.yaml +nextflow run bigbio/quantms -profile docker -params-file params.yaml ``` with: @@ -100,14 +100,14 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: ```bash -nextflow pull nf-core/quantms +nextflow pull bigbio/quantms ``` ### Reproducibility It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. -First, go to the [nf-core/quantms releases page](https://github.com/nf-core/quantms/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. +First, go to the [bigbio/quantms releases page](https://github.com/bigbio/quantms/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. diff --git a/main.nf b/main.nf index 973c7e4d..82d3a55f 100644 --- a/main.nf +++ b/main.nf @@ -1,9 +1,9 @@ #!/usr/bin/env nextflow /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - nf-core/quantms + bigbio/quantms ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Github : https://github.com/nf-core/quantms + Github : https://github.com/bigbio/quantms Website: https://nf-co.re/quantms Slack : https://nfcore.slack.com/channels/quantms ---------------------------------------------------------------------------------------- @@ -40,7 +40,7 @@ params.fasta = getGenomeAttribute('fasta') // // WORKFLOW: Run main analysis pipeline depending on type of input // -workflow NFCORE_QUANTMS { +workflow BIGBIO_QUANTMS { take: samplesheet // channel: samplesheet read in from --input @@ -80,7 +80,7 @@ workflow { // // WORKFLOW: Run main workflow // - NFCORE_QUANTMS ( + BIGBIO_QUANTMS ( PIPELINE_INITIALISATION.out.samplesheet ) // @@ -93,7 +93,7 @@ workflow { params.outdir, params.monochrome_logs, params.hook_url, - NFCORE_QUANTMS.out.multiqc_report + BIGBIO_QUANTMS.out.multiqc_report ) } diff --git a/modules.json b/modules.json index 68be23fc..ad8cd4c5 100644 --- a/modules.json +++ b/modules.json @@ -1,6 +1,6 @@ { - "name": "nf-core/quantms", - "homePage": "https://github.com/nf-core/quantms", + "name": "bigbio/quantms", + "homePage": "https://github.com/bigbio/quantms", "repos": { "https://github.com/nf-core/modules.git": { "modules": { diff --git a/nextflow.config b/nextflow.config index 75bd3c3c..3e95f566 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - nf-core/quantms Nextflow config file + bigbio/quantms Nextflow config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Default config options for all compute environments ---------------------------------------------------------------------------------------- @@ -167,7 +167,7 @@ profiles { // Load nf-core custom profiles from different Institutions includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" -// Load nf-core/quantms custom profiles from different institutions. +// Load bigbio/quantms custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/quantms.config" : "/dev/null" @@ -225,7 +225,7 @@ dag { } manifest { - name = 'nf-core/quantms' + name = 'bigbio/quantms' author = """Yasset Perez-Riverol""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead contributors = [ // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 @@ -238,7 +238,7 @@ manifest { orcid: '' ], ] - homePage = 'https://github.com/nf-core/quantms' + homePage = 'https://github.com/bigbio/quantms' description = """Quantitative Mass Spectrometry nf-core workflow""" mainScript = 'main.nf' defaultBranch = 'master' @@ -257,7 +257,7 @@ validation { monochromeLogs = params.monochrome_logs help { enabled = true - command = "nextflow run nf-core/quantms -profile --input samplesheet.csv --outdir " + command = "nextflow run bigbio/quantms -profile --input samplesheet.csv --outdir " fullParameter = "help_full" showHiddenParameter = "show_hidden" beforeText = """ @@ -267,7 +267,7 @@ validation { \033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m \033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m \033[0;32m`._,._,\'\033[0m -\033[0;35m nf-core/quantms ${manifest.version}\033[0m +\033[0;35m bigbio/quantms ${manifest.version}\033[0m -\033[2m----------------------------------------------------\033[0m- """ afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} @@ -275,7 +275,7 @@ validation { https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/nf-core/quantms/blob/master/CITATIONS.md + https://github.com/bigbio/quantms/blob/master/CITATIONS.md """ } summary { diff --git a/nextflow_schema.json b/nextflow_schema.json index d0c5e349..0e599ee8 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/quantms/master/nextflow_schema.json", - "title": "nf-core/quantms pipeline parameters", + "$id": "https://raw.githubusercontent.com/bigbio/quantms/master/nextflow_schema.json", + "title": "bigbio/quantms pipeline parameters", "description": "Quantitative Mass Spectrometry nf-core workflow", "type": "object", "$defs": { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 73dad181..be0d04b7 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2024-12-20T10:14:05+00:00", - "description": "

\n \n \n \"nf-core/quantms\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/quantms/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/quantms/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/quantms/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/quantms/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/quantms/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/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/quantms)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23quantms-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/quantms)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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/quantms** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\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/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-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/quantms \\\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/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/quantms/usage) and the [parameter documentation](https://nf-co.re/quantms/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/quantms/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/quantms/output).\n\n## Credits\n\nnf-core/quantms was originally written by Yasset Perez-Riverol.\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](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#quantms` channel](https://nfcore.slack.com/channels/quantms) (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": "2024-12-20T16:31:51+00:00", + "description": "

\n \n \n \"bigbio/quantms\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/bigbio/quantms/actions/workflows/ci.yml/badge.svg)](https://github.com/bigbio/quantms/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/bigbio/quantms/actions/workflows/linting.yml/badge.svg)](https://github.com/bigbio/quantms/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/quantms/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/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/bigbio/quantms)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23quantms-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/quantms)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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**bigbio/quantms** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\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/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-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 bigbio/quantms \\\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/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/quantms/usage) and the [parameter documentation](https://nf-co.re/quantms/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/quantms/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/quantms/output).\n\n## Credits\n\nbigbio/quantms was originally written by Yasset Perez-Riverol.\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](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#quantms` channel](https://nfcore.slack.com/channels/quantms) (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" @@ -92,17 +92,17 @@ "@id": ".prettierignore" } ], - "isBasedOn": "https://github.com/nf-core/quantms", + "isBasedOn": "https://github.com/bigbio/quantms", "license": "MIT", "mainEntity": { "@id": "main.nf" }, "mentions": [ { - "@id": "#4daec247-b84a-4b88-876c-0488b747c718" + "@id": "#0a8f3b24-fec3-4675-af6b-ef0c167e9833" } ], - "name": "nf-core/quantms" + "name": "bigbio/quantms" }, { "@id": "ro-crate-metadata.json", @@ -128,7 +128,7 @@ } ], "dateCreated": "", - "dateModified": "2024-12-20T10:14:05Z", + "dateModified": "2024-12-20T16:31:51Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -148,14 +148,14 @@ "@id": "https://orcid.org/0000-0001-6579-6941" } ], - "name": ["nf-core/quantms"], + "name": ["bigbio/quantms"], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": ["https://github.com/nf-core/quantms", "https://nf-co.re/quantms/dev/"], + "url": ["https://github.com/bigbio/quantms", "https://nf-co.re/bigbio/quantms/dev/"], "version": ["1.3.1dev"] }, { @@ -171,23 +171,23 @@ "version": "!>=24.04.2" }, { - "@id": "#4daec247-b84a-4b88-876c-0488b747c718", + "@id": "#0a8f3b24-fec3-4675-af6b-ef0c167e9833", "@type": "TestSuite", "instance": [ { - "@id": "#bcfce862-330d-4b76-82dd-09667e3572d4" + "@id": "#11e2d024-5c5d-438d-8531-3e6791acb3c1" } ], "mainEntity": { "@id": "main.nf" }, - "name": "Test suite for nf-core/quantms" + "name": "Test suite for bigbio/quantms" }, { - "@id": "#bcfce862-330d-4b76-82dd-09667e3572d4", + "@id": "#11e2d024-5c5d-438d-8531-3e6791acb3c1", "@type": "TestInstance", - "name": "GitHub Actions workflow for testing nf-core/quantms", - "resource": "repos/nf-core/quantms/actions/workflows/ci.yml", + "name": "GitHub Actions workflow for testing bigbio/quantms", + "resource": "repos/bigbio/quantms/actions/workflows/ci.yml", "runsOn": { "@id": "https://w3id.org/ro/terms/test#GithubService" }, diff --git a/subworkflows/local/utils_nfcore_quantms_pipeline/main.nf b/subworkflows/local/utils_nfcore_quantms_pipeline/main.nf index 5cb04435..7cad3f97 100644 --- a/subworkflows/local/utils_nfcore_quantms_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_quantms_pipeline/main.nf @@ -1,5 +1,5 @@ // -// Subworkflow with functionality specific to the nf-core/quantms pipeline +// Subworkflow with functionality specific to the bigbio/quantms pipeline // /* From 1ebbef0573e0f054d94dc7e3054dba22907ac437 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 20 Dec 2024 17:03:31 +0000 Subject: [PATCH 03/11] template 3.1.0 update --- .github/CONTRIBUTING.md | 6 +++--- .github/workflows/awsfulltest.yml | 0 .github/workflows/awstest.yml | 0 CHANGELOG.md | 10 ++++----- README.md | 28 +++++++++++++------------- assets/multiqc_config.yml | 2 +- conf/dev.config | 2 +- conf/test_dda_id.config | 2 +- conf/test_dia.config | 2 +- conf/test_full_dia.config | 2 +- conf/test_full_lfq.config | 2 +- conf/test_full_tmt.config | 2 +- conf/test_latest_dia.config | 2 +- conf/test_lfq.config | 2 +- conf/test_lfq_sage.config | 2 +- conf/test_localize.config | 2 +- conf/test_tmt.config | 2 +- conf/test_tmt_corr.config | 2 +- docs/usage.md | 6 +++--- main.nf | 8 ++++---- modules/local/samplesheet_check.nf | 2 +- nextflow.config | 4 ++-- subworkflows/local/file_preparation.nf | 2 +- workflows/quantms.nf | 2 +- 24 files changed, 47 insertions(+), 47 deletions(-) delete mode 100644 .github/workflows/awsfulltest.yml delete mode 100644 .github/workflows/awstest.yml diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 925638d6..511a6ac0 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -10,13 +10,13 @@ However, don't be put off by this template - other more general issues and sugge Contributions to the code are even more welcome ;) > [!NOTE] -> If you need help using or modifying nf-core/quantms or bigbio/quantms then the best place to ask is on the nf-core Slack [#quantms](https://nfcore.slack.com/channels/quantms) channel ([join our Slack here](https://nf-co.re/join/slack)). +> If you need help using or modifying bigbio/quantms or bigbio/quantms then the best place to ask is on the nf-core Slack [#quantms](https://nfcore.slack.com/channels/quantms) channel ([join our Slack here](https://nf-co.re/join/slack)). ## Contribution workflow -If you'd like to write some code for nf-core/quantms and bigbio/quantms, the standard workflow is as follows: +If you'd like to write some code for bigbio/quantms and bigbio/quantms, the standard workflow is as follows: -1. Check that there isn't already an issue about your idea in the [nf-core/quantms issues](https://github.com/nf-core/quantms/issues) and [bigbio/quantms_issues](https://github.com/bigbio/quantms/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this +1. Check that there isn't already an issue about your idea in the [bigbio/quantms issues](https://github.com/bigbio/quantms/issues) and [bigbio/quantms_issues](https://github.com/bigbio/quantms/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [bigbio/quantms repository](https://github.com/bigbio/quantms) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) 4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml deleted file mode 100644 index e69de29b..00000000 diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml deleted file mode 100644 index e69de29b..00000000 diff --git a/CHANGELOG.md b/CHANGELOG.md index 59cdba42..feec1b99 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -125,16 +125,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` -- [#92](https://github.com/nf-core/quantms/pull/92) Improved output docs for mzTab -- [#91](https://github.com/nf-core/quantms/pull/91) Added dev profile for nightly versions of OpenMS tools +- [#92](https://github.com/bigbio/quantms/pull/92) Improved output docs for mzTab +- [#91](https://github.com/bigbio/quantms/pull/91) Added dev profile for nightly versions of OpenMS tools ### `Changed` -- [#88](https://github.com/nf-core/quantms/pull/88) Updated Comet version to latest release (2023010) +- [#88](https://github.com/bigbio/quantms/pull/88) Updated Comet version to latest release (2023010) ### `Fixed` -- [#93](https://github.com/nf-core/quantms/pull/93) Fixed bug in docker vs. singularity container logic in some processes. +- [#93](https://github.com/bigbio/quantms/pull/93) Fixed bug in docker vs. singularity container logic in some processes. ## [1.1.0] nfcore/quantms - [03/20/2023] - Berlin @@ -176,7 +176,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [1.0] nfcore/quantms - [05/02/2022] - Havana -Initial release of nf-core/quantms, created with the [nf-core](https://nf-co.re/) template. +Initial release of bigbio/quantms, created with the [nf-core](https://nf-co.re/) template. ### `Added` diff --git a/README.md b/README.md index 67a1afa7..d86ef492 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ -# ![nf-core/quantms](docs/images/nf-core-quantms_logo_light.png#gh-light-mode-only) ![nf-core/quantms](docs/images/nf-core-quantms_logo_dark.png#gh-dark-mode-only) +# ![bigbio/quantms](docs/images/nf-core-quantms_logo_light.png#gh-light-mode-only) ![bigbio/quantms](docs/images/nf-core-quantms_logo_dark.png#gh-dark-mode-only) [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/quantms/results)[![Cite with Zenodo](https://img.shields.io/badge/DOI-10.5281/zenodo.7754148-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7754148) -[![GitHub Actions CI Status](https://github.com/nf-core/quantms/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/quantms/actions/workflows/ci.yml) -[![GitHub Actions Linting Status](https://github.com/nf-core/quantms/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/quantms/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/quantms/results)[![Cite with Zenodo](https://img.shields.io/badge/DOI-10.5281/zenodo.7754148-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7754148) +[![GitHub Actions CI Status](https://github.com/bigbio/quantms/actions/workflows/ci.yml/badge.svg)](https://github.com/bigbio/quantms/actions/workflows/ci.yml) +[![GitHub Actions Linting Status](https://github.com/bigbio/quantms/actions/workflows/linting.yml/badge.svg)](https://github.com/bigbio/quantms/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/quantms/results)[![Cite with Zenodo](https://img.shields.io/badge/DOI-10.5281/zenodo.7754148-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7754148) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) @@ -15,10 +15,10 @@ ## Introduction -**nf-core/quantms** is a bioinformatics best-practice analysis pipeline for Quantitative Mass Spectrometry (MS). Currently, the workflow supports three major MS-based analytical methods: (i) Data dependant acquisition (DDA) label-free and Isobaric quantitation (e.g. TMT, iTRAQ); (ii) Data independent acquisition (DIA) label-free quantification (for details see our in-depth documentation on [quantms](https://quantms.readthedocs.io/en/latest/)). +**bigbio/quantms** is a bioinformatics best-practice analysis pipeline for Quantitative Mass Spectrometry (MS). Currently, the workflow supports three major MS-based analytical methods: (i) Data dependant acquisition (DDA) label-free and Isobaric quantitation (e.g. TMT, iTRAQ); (ii) Data independent acquisition (DIA) label-free quantification (for details see our in-depth documentation on [quantms](https://quantms.readthedocs.io/en/latest/)).

- nf-core/quantms workflow overview + bigbio/quantms workflow overview

The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! @@ -29,14 +29,14 @@ On release, automated continuous integration tests run the pipeline on a full-si ## Pipeline summary -**nf-core/quantms** allows uses to perform analyses of three main types of analytical mass spectrometry-based quantitative methods: DDA-LFQ, DDA-ISO, DIA-LFQ. Each of these workflows share some processes but also includes their own steps. In summary: +**bigbio/quantms** allows uses to perform analyses of three main types of analytical mass spectrometry-based quantitative methods: DDA-LFQ, DDA-ISO, DIA-LFQ. Each of these workflows share some processes but also includes their own steps. In summary: ### DDA-LFQ (data-dependent label-free quantification) 1. RAW file conversion to mzML ([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser)) 2. Peptide identification using [`comet`](https://uwpr.github.io/Comet/) and/or [`msgf+`](https://github.com/MSGFPlus/msgfplus) 3. Re-scoring peptide identifications [`percolator`](https://github.com/percolator/percolator) -4. Peptide identification FDR [`openms fdr tool`](https://github.com/nf-core/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf) +4. Peptide identification FDR [`openms fdr tool`](https://github.com/bigbio/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf) 5. Modification localization [`luciphor`](https://github.com/dfermin/lucXor) 6. Quantification: Feature detection [`proteomicsLFQ`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_ProteomicsLFQ.html) 7. Protein inference and quantification [`proteomicsLFQ`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_ProteomicsLFQ.html) @@ -48,7 +48,7 @@ On release, automated continuous integration tests run the pipeline on a full-si 1. RAW file conversion to mzML ([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser)) 2. Peptide identification using [`comet`](https://uwpr.github.io/Comet/) and/or [`msgf+`](https://github.com/MSGFPlus/msgfplus) 3. Re-scoring peptide identifications [`percolator`](https://github.com/percolator/percolator) -4. Peptide identification FDR [`openms fdr tool`](https://github.com/nf-core/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf) +4. Peptide identification FDR [`openms fdr tool`](https://github.com/bigbio/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf) 5. Modification localization [`luciphor`](https://github.com/dfermin/lucXor) 6. Extracts and normalizes isobaric labeling [`IsobaricAnalyzer`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html) 7. Protein inference [`ProteinInference`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteinInference.html) or [`Epifany`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_Epifany.html) for bayesian inference. @@ -59,7 +59,7 @@ On release, automated continuous integration tests run the pipeline on a full-si ### DIA-LFQ (data-independent label-free quantification) 1. RAW file conversion to mzML when RAW as input([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser)) -2. Performing an [optional step](https://github.com/nf-core/quantms/blob/dev/modules/local/tdf2mzml/main.nf): Converting .d to mzML when bruker data as input and set `convert_dotd` to true +2. Performing an [optional step](https://github.com/bigbio/quantms/blob/dev/modules/local/tdf2mzml/main.nf): Converting .d to mzML when bruker data as input and set `convert_dotd` to true 3. DIA-NN analysis [`dia-nn`](https://github.com/vdemichev/DiaNN/) 4. Generation of output files (msstats) 5. QC reports generation [`pmultiqc`](https://github.com/bigbio/pmultiqc) @@ -69,7 +69,7 @@ On release, automated continuous integration tests run the pipeline on a full-si A graphical overview of suggested routes through the pipeline depending on context can be seen below.

- nf-core/quantms metro map + bigbio/quantms metro map

## Usage @@ -90,7 +90,7 @@ Now, you can run the pipeline using: ```bash -nextflow run nf-core/quantms \ +nextflow run bigbio/quantms \ -profile \ --input project.sdrf.tsv \ --database database.fasta \ @@ -105,7 +105,7 @@ For more details and further functionality, please refer to the [usage documenta ## Additional documentation and tutorial -The **nf-core/quantms** pipeline comes with a stand-alone [full documentation](https://quantms.readthedocs.io/en/latest/) including examples, benchmarks, and detailed explanation about the data analysis of proteomics data using quantms. +The **bigbio/quantms** pipeline comes with a stand-alone [full documentation](https://quantms.readthedocs.io/en/latest/) including examples, benchmarks, and detailed explanation about the data analysis of proteomics data using quantms. ## Pipeline output @@ -115,7 +115,7 @@ For more details about the output files and reports, please refer to the ## Credits -nf-core/quantms was originally written by: Chengxin Dai ([@daichengxin](https://github.com/daichengxin)), Julianus Pfeuffer ([@jpfeuffer](https://github.com/jpfeuffer)) and Yasset Perez-Riverol ([@ypriverol](https://github.com/ypriverol)). +bigbio/quantms was originally written by: Chengxin Dai ([@daichengxin](https://github.com/daichengxin)), Julianus Pfeuffer ([@jpfeuffer](https://github.com/jpfeuffer)) and Yasset Perez-Riverol ([@ypriverol](https://github.com/ypriverol)). We thank the following people for their extensive assistance in the development of this pipeline: @@ -141,7 +141,7 @@ If you use **bigbio/quantms** for your analysis, please cite it using the follow ## Other citations - + diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f39393c7..e8475682 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/quantms + This report has been generated by the bigbio/quantms analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: diff --git a/conf/dev.config b/conf/dev.config index 076e14c7..0b9de68e 100644 --- a/conf/dev.config +++ b/conf/dev.config @@ -6,7 +6,7 @@ executable and thirdparty containers. Use as follows: - nextflow run nf-core/quantms -profile dev, [--outdir ] + nextflow run bigbio/quantms -profile dev, [--outdir ] ------------------------------------------------------------------------------------------- */ diff --git a/conf/test_dda_id.config b/conf/test_dda_id.config index 4f6dcc97..072d9531 100644 --- a/conf/test_dda_id.config +++ b/conf/test_dda_id.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a real and full-size test. Use as follows: - nextflow run nf-core/quantms -profile test_dda_id, [--outdir ] + nextflow run bigbio/quantms -profile test_dda_id, [--outdir ] ------------------------------------------------------------------------------------------------ */ diff --git a/conf/test_dia.config b/conf/test_dia.config index ce041b92..2bd1510b 100644 --- a/conf/test_dia.config +++ b/conf/test_dia.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple test. Use as follows: - nextflow run nf-core/quantms -profile test_dia, [--outdir ] + nextflow run bigbio/quantms -profile test_dia, [--outdir ] ------------------------------------------------------------------------------------------------ */ diff --git a/conf/test_full_dia.config b/conf/test_full_dia.config index 2bfb1142..0d421b53 100644 --- a/conf/test_full_dia.config +++ b/conf/test_full_dia.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a real and full-size test. Use as follows: - nextflow run nf-core/quantms -profile test_full_dia, [--outdir ] + nextflow run bigbio/quantms -profile test_full_dia, [--outdir ] ------------------------------------------------------------------------------------------------ */ diff --git a/conf/test_full_lfq.config b/conf/test_full_lfq.config index e49a6d07..c028754b 100644 --- a/conf/test_full_lfq.config +++ b/conf/test_full_lfq.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a real and full-size test. Use as follows: - nextflow run nf-core/quantms -profile test_full_lfq, [--outdir ] + nextflow run bigbio/quantms -profile test_full_lfq, [--outdir ] ------------------------------------------------------------------------------------------------ */ diff --git a/conf/test_full_tmt.config b/conf/test_full_tmt.config index 5f418f55..3262f160 100644 --- a/conf/test_full_tmt.config +++ b/conf/test_full_tmt.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run nf-core/quantms -profile test_full_tmt, [--outdir ] + nextflow run bigbio/quantms -profile test_full_tmt, [--outdir ] ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_latest_dia.config b/conf/test_latest_dia.config index 7ec11563..f7c047f2 100644 --- a/conf/test_latest_dia.config +++ b/conf/test_latest_dia.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple test. Use as follows: - nextflow run nf-core/quantms -profile test_dia, [--outdir ] + nextflow run bigbio/quantms -profile test_dia, [--outdir ] ------------------------------------------------------------------------------------------------ */ diff --git a/conf/test_lfq.config b/conf/test_lfq.config index d91f7ae6..d550fc07 100644 --- a/conf/test_lfq.config +++ b/conf/test_lfq.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple test. Use as follows: - nextflow run nf-core/quantms -profile test_lfq, [--outdir ] + nextflow run bigbio/quantms -profile test_lfq, [--outdir ] ------------------------------------------------------------------------------------------------ */ diff --git a/conf/test_lfq_sage.config b/conf/test_lfq_sage.config index a59a8f62..bd267261 100644 --- a/conf/test_lfq_sage.config +++ b/conf/test_lfq_sage.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple test. Use as follows: - nextflow run nf-core/quantms -profile test_lfq, [--outdir ] + nextflow run bigbio/quantms -profile test_lfq, [--outdir ] ------------------------------------------------------------------------------------------------ */ diff --git a/conf/test_localize.config b/conf/test_localize.config index 32d6bb6f..b59103aa 100644 --- a/conf/test_localize.config +++ b/conf/test_localize.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple test. Use as follows: - nextflow run nf-core/quantms -profile test_localize, [--outdir ] + nextflow run bigbio/quantms -profile test_localize, [--outdir ] ---------------------------------------------------------------------------------------------------- */ diff --git a/conf/test_tmt.config b/conf/test_tmt.config index 916f9b94..f0d52349 100644 --- a/conf/test_tmt.config +++ b/conf/test_tmt.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run nf-core/quantms -profile test_tmt, [--outdir ] + nextflow run bigbio/quantms -profile test_tmt, [--outdir ] ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_tmt_corr.config b/conf/test_tmt_corr.config index 5be84ea4..757d9102 100644 --- a/conf/test_tmt_corr.config +++ b/conf/test_tmt_corr.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run nf-core/quantms -profile test_tmt, [--outdir ] + nextflow run bigbio/quantms -profile test_tmt, [--outdir ] ---------------------------------------------------------------------------------------- */ diff --git a/docs/usage.md b/docs/usage.md index 80a0bef4..6c85d3f9 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -11,7 +11,7 @@ The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/quantms --input '/url/path/to/your/experiment_design.sdrf.tsv' --database '/url/path/to/your/proteindatabase.fasta' --outdir './results' -profile docker +nextflow run bigbio/quantms --input '/url/path/to/your/experiment_design.sdrf.tsv' --database '/url/path/to/your/proteindatabase.fasta' --outdir './results' -profile docker ``` where the experimental design file has to be one of: @@ -62,14 +62,14 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: ```bash -nextflow pull nf-core/quantms +nextflow pull bigbio/quantms ``` ### Reproducibility It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. -First, go to the [nf-core/quantms releases page](https://github.com/nf-core/quantms/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. +First, go to the [bigbio/quantms releases page](https://github.com/bigbio/quantms/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. diff --git a/main.nf b/main.nf index 4a12873d..fa66ac9a 100644 --- a/main.nf +++ b/main.nf @@ -20,9 +20,9 @@ include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_quan include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_quantms_pipeline' // -// WORKFLOW: Run main nf-core/quantms analysis pipeline +// WORKFLOW: Run main bigbio/quantms analysis pipeline // -workflow NFCORE_QUANTMS { +workflow BIGBIO_QUANTMS { main: @@ -46,7 +46,7 @@ workflow { main: - NFCORE_QUANTMS () + BIGBIO_QUANTMS () // // SUBWORKFLOW: Run completion tasks @@ -58,7 +58,7 @@ workflow { params.outdir, params.monochrome_logs, params.hook_url, - NFCORE_QUANTMS.out.multiqc_report + BIGBIO_QUANTMS.out.multiqc_report ) } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index b500ab0a..76b16613 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -21,7 +21,7 @@ process SAMPLESHEET_CHECK { when: task.ext.when == null || task.ext.when - script: // This script is bundled with the pipeline, in nf-core/quantms/bin/ + script: // This script is bundled with the pipeline, in bigbio/quantms/bin/ // TODO validate experimental design file def args = task.ext.args ?: '' def string_skip_sdrf_validation = params.validate_ontologies == false ? "--skip_sdrf_validation" : "" diff --git a/nextflow.config b/nextflow.config index dd1b96c9..17fda145 100644 --- a/nextflow.config +++ b/nextflow.config @@ -403,7 +403,7 @@ profiles { // Load nf-core custom profiles from different Institutions includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" -// Load nf-core/quantms custom profiles from different institutions. +// Load bigbio/quantms custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/quantms.config" : "/dev/null" @@ -458,7 +458,7 @@ dag { } manifest { - name = 'nf-core/quantms' + name = 'bigbio/quantms' author = """Yasset Perez-Riverol""" homePage = 'https://github.com/bigbio/quantms' author = """Yasset Perez-Riverol""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead diff --git a/subworkflows/local/file_preparation.nf b/subworkflows/local/file_preparation.nf index 5217b977..63250560 100644 --- a/subworkflows/local/file_preparation.nf +++ b/subworkflows/local/file_preparation.nf @@ -46,7 +46,7 @@ workflow FILE_PREPARATION { // Note: we used to always index mzMLs if not already indexed but due to // either a bug or limitation in nextflow // peeking into a remote file consumes a lot of RAM - // See https://github.com/nf-core/quantms/issues/61 + // See https://github.com/bigbio/quantms/issues/61 // This is now done in the search engines themselves if they need it. // This means users should pre-index to save time and space, especially // when re-running. diff --git a/workflows/quantms.nf b/workflows/quantms.nf index 3c7492ad..ebd64b60 100644 --- a/workflows/quantms.nf +++ b/workflows/quantms.nf @@ -75,7 +75,7 @@ workflow QUANTMS { } .set{ch_fileprep_result} // - // WORKFLOW: Run main nf-core/quantms analysis pipeline based on the quantification type + // WORKFLOW: Run main bigbio/quantms analysis pipeline based on the quantification type // ch_pipeline_results = Channel.empty() ch_ids_pmultiqc = Channel.empty() From c6d809161e1bcc92b756307b966aa2f3de88c783 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 20 Dec 2024 17:07:44 +0000 Subject: [PATCH 04/11] Template update for nf-core/tools version 3.1.1 --- .editorconfig | 4 ++ .github/ISSUE_TEMPLATE/bug_report.yml | 1 - .github/workflows/download_pipeline.yml | 41 +++++++++++-------- .nf-core.yml | 2 +- .prettierignore | 1 + CITATIONS.md | 4 +- LICENSE | 2 +- README.md | 15 ++----- docs/output.md | 11 ++--- docs/usage.md | 2 +- nextflow.config | 3 ++ ro-crate-metadata.json | 39 ++++++++++++------ .../utils_nfcore_quantms_pipeline/main.nf | 2 +- 13 files changed, 71 insertions(+), 56 deletions(-) diff --git a/.editorconfig b/.editorconfig index 72dda289..6d9b74cc 100644 --- a/.editorconfig +++ b/.editorconfig @@ -31,3 +31,7 @@ indent_size = unset # ignore python and markdown [*.{py,md}] indent_style = unset + +# ignore ro-crate metadata files +[**/ro-crate-metadata.json] +insert_final_newline = unset diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 48f4ce30..b8f3a354 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -9,7 +9,6 @@ body: - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [bigbio/quantms pipeline documentation](https://nf-co.re/quantms/usage) - - type: textarea id: description attributes: diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2576cc0c..13b51e2c 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -28,8 +28,12 @@ env: NXF_ANSI_LOG: false jobs: - download: + configure: runs-on: ubuntu-latest + outputs: + REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} + REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} + REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }} steps: - name: Install Nextflow uses: nf-core/setup-nextflow@v2 @@ -53,22 +57,27 @@ jobs: pip install git+https://github.com/nf-core/tools.git@dev - name: Get the repository name and current branch set as environment variable + id: get_repo_properties run: | - echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} - echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" - name: Make a cache directory for the container images run: | mkdir -p ./singularity_container_images + download: + runs-on: ubuntu-latest + needs: configure + steps: - name: Download the pipeline env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ - --revision ${{ env.REPO_BRANCH }} \ - --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \ + --revision ${{ needs.configure.outputs.REPO_BRANCH }} \ + --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \ @@ -76,14 +85,14 @@ jobs: --download-configuration 'yes' - name: Inspect download - run: tree ./${{ env.REPOTITLE_LOWERCASE }} + run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} - name: Count the downloaded number of container images id: count_initial run: | image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) echo "Initial container image count: $image_count" - echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT" - name: Run the downloaded pipeline (stub) id: stub_run_pipeline @@ -91,27 +100,27 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline - if: ${{ job.steps.stub_run_pipeline.status == failure() }} + if: ${{ steps.stub_run_pipeline.outcome == 'failure' }} env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results - name: Count the downloaded number of container images id: count_afterwards run: | image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) echo "Post-pipeline run container image count: $image_count" - echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" - name: Compare container image counts run: | - if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then - initial_count=${{ env.IMAGE_COUNT_INITIAL }} - final_count=${{ env.IMAGE_COUNT_AFTER }} + if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} + final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }} difference=$((final_count - initial_count)) echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" tree ./singularity_container_images diff --git a/.nf-core.yml b/.nf-core.yml index d6cb9511..83f691af 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -13,7 +13,7 @@ lint: - docs/README.md multiqc_config: false nextflow_config: false -nf_core_version: 3.1.0 +nf_core_version: 3.1.1 repository_type: pipeline template: author: Yasset Perez-Riverol diff --git a/.prettierignore b/.prettierignore index 437d763d..edd29f01 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,3 +10,4 @@ testing/ testing* *.pyc bin/ +ro-crate-metadata.json diff --git a/CITATIONS.md b/CITATIONS.md index 8cf8ea3c..2c9f8512 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,9 +12,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - -- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. diff --git a/LICENSE b/LICENSE index dd513e01..c29ac178 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) Yasset Perez-Riverol +Copyright (c) The bigbio/quantms team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 2411c623..0bfec08d 100644 --- a/README.md +++ b/README.md @@ -3,9 +3,7 @@ bigbio/quantms - - -[![GitHub Actions CI Status](https://github.com/bigbio/quantms/actions/workflows/ci.yml/badge.svg)](https://github.com/bigbio/quantms/actions/workflows/ci.yml) +[![GitHub Actions CI Status](https://github.com/bigbio/quantms/actions/workflows/ci.yml/badge.svg)](https://github.com/bigbio/quantms/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/bigbio/quantms/actions/workflows/linting.yml/badge.svg)](https://github.com/bigbio/quantms/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/quantms/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) @@ -29,15 +27,12 @@ - - -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage > [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - - - + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/docs/output.md b/docs/output.md index 2de6349e..9f7beeac 100644 --- a/docs/output.md +++ b/docs/output.md @@ -12,8 +12,7 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: -- [FastQC](#fastqc) - Raw read QC -- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline +- [FastQC](#fastqc) - Raw read QC- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC @@ -27,9 +26,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d -[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). - -### MultiQC +[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).### MultiQC
Output files @@ -43,9 +40,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . - -### Pipeline information +Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see .### Pipeline information
Output files diff --git a/docs/usage.md b/docs/usage.md index e2def00a..4d30993c 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -130,7 +130,7 @@ Several generic profiles are bundled with the pipeline which instruct the pipeli > [!IMPORTANT] > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is suported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). +The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. diff --git a/nextflow.config b/nextflow.config index 3e95f566..707bc849 100644 --- a/nextflow.config +++ b/nextflow.config @@ -283,3 +283,6 @@ validation { afterText = validation.help.afterText } } + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index be0d04b7..c0a07921 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2024-12-20T16:31:51+00:00", - "description": "

\n \n \n \"bigbio/quantms\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/bigbio/quantms/actions/workflows/ci.yml/badge.svg)](https://github.com/bigbio/quantms/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/bigbio/quantms/actions/workflows/linting.yml/badge.svg)](https://github.com/bigbio/quantms/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/quantms/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/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/bigbio/quantms)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23quantms-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/quantms)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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**bigbio/quantms** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\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/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-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 bigbio/quantms \\\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/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/quantms/usage) and the [parameter documentation](https://nf-co.re/quantms/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/quantms/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/quantms/output).\n\n## Credits\n\nbigbio/quantms was originally written by Yasset Perez-Riverol.\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](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#quantms` channel](https://nfcore.slack.com/channels/quantms) (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": "2024-12-20T17:07:41+00:00", + "description": "

\n \n \n \"bigbio/quantms\"\n \n

[![GitHub Actions CI Status](https://github.com/bigbio/quantms/actions/workflows/ci.yml/badge.svg)](https://github.com/bigbio/quantms/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/bigbio/quantms/actions/workflows/linting.yml/badge.svg)](https://github.com/bigbio/quantms/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/quantms/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/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/bigbio/quantms)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23quantms-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/quantms)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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**bigbio/quantms** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. 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/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-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 bigbio/quantms \\\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/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/quantms/usage) and the [parameter documentation](https://nf-co.re/quantms/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/quantms/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/quantms/output).\n\n## Credits\n\nbigbio/quantms was originally written by Yasset Perez-Riverol.\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](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#quantms` channel](https://nfcore.slack.com/channels/quantms) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\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": "#0a8f3b24-fec3-4675-af6b-ef0c167e9833" + "@id": "#afca89bf-d52c-494d-aa93-4b2b9cdcf80c" } ], "name": "bigbio/quantms" @@ -121,14 +121,18 @@ }, { "@id": "main.nf", - "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], "creator": [ { "@id": "https://orcid.org/0000-0001-6579-6941" } ], "dateCreated": "", - "dateModified": "2024-12-20T16:31:51Z", + "dateModified": "2024-12-20T17:07:41Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -142,21 +146,30 @@ "proteomics", "tmt" ], - "license": ["MIT"], + "license": [ + "MIT" + ], "maintainer": [ { "@id": "https://orcid.org/0000-0001-6579-6941" } ], - "name": ["bigbio/quantms"], + "name": [ + "bigbio/quantms" + ], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": ["https://github.com/bigbio/quantms", "https://nf-co.re/bigbio/quantms/dev/"], - "version": ["1.3.1dev"] + "url": [ + "https://github.com/bigbio/quantms", + "https://nf-co.re/bigbio/quantms/dev/" + ], + "version": [ + "1.3.1dev" + ] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -171,11 +184,11 @@ "version": "!>=24.04.2" }, { - "@id": "#0a8f3b24-fec3-4675-af6b-ef0c167e9833", + "@id": "#afca89bf-d52c-494d-aa93-4b2b9cdcf80c", "@type": "TestSuite", "instance": [ { - "@id": "#11e2d024-5c5d-438d-8531-3e6791acb3c1" + "@id": "#715e99e2-ff15-45fb-90a4-f35e18316436" } ], "mainEntity": { @@ -184,7 +197,7 @@ "name": "Test suite for bigbio/quantms" }, { - "@id": "#11e2d024-5c5d-438d-8531-3e6791acb3c1", + "@id": "#715e99e2-ff15-45fb-90a4-f35e18316436", "@type": "TestInstance", "name": "GitHub Actions workflow for testing bigbio/quantms", "resource": "repos/bigbio/quantms/actions/workflows/ci.yml", @@ -319,4 +332,4 @@ "name": "Yasset Perez-Riverol" } ] -} +} \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_quantms_pipeline/main.nf b/subworkflows/local/utils_nfcore_quantms_pipeline/main.nf index 7cad3f97..7297ba63 100644 --- a/subworkflows/local/utils_nfcore_quantms_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_quantms_pipeline/main.nf @@ -117,7 +117,7 @@ workflow PIPELINE_COMPLETION { main: summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") def multiqc_reports = multiqc_report.toList() - + // // Completion email and summary // From 5a70360f33955f7b45c0faa259f37efdc45c89c0 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 20 Dec 2024 17:19:24 +0000 Subject: [PATCH 05/11] template 3.1.0 update --- conf/modules.config | 4 ++-- conf/test_dia.config | 2 +- conf/test_latest_dia.config | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 9cb01f92..f2a4f287 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -20,7 +20,7 @@ process { // Local Subworkflows // INPUT_CHECK - withName: 'NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK' { + withName: 'BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK' { publishDir = [ path: { "${params.outdir}/pipeline_info" }, mode: 'copy', @@ -28,7 +28,7 @@ process { ] } - withName: 'NFCORE_QUANTMS:QUANTMS:CUSTOM_DUMPSOFTWAREVERSIONS' { + withName: 'BIGBIO_QUANTMS:QUANTMS:CUSTOM_DUMPSOFTWAREVERSIONS' { publishDir = [ path: { "${params.outdir}/pipeline_info" }, mode: params.publish_dir_mode, diff --git a/conf/test_dia.config b/conf/test_dia.config index 2bd1510b..5f90dfc0 100644 --- a/conf/test_dia.config +++ b/conf/test_dia.config @@ -42,7 +42,7 @@ params { process { // thermorawfileparser - withName: 'NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER' { + withName: 'BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER' { publishDir = [path: { "${params.outdir}/${task.process.tokenize(':')[-1].toLowerCase()}" }, pattern: "*.log" ] } } diff --git a/conf/test_latest_dia.config b/conf/test_latest_dia.config index f7c047f2..72dad9dc 100644 --- a/conf/test_latest_dia.config +++ b/conf/test_latest_dia.config @@ -35,7 +35,7 @@ params { process { // thermorawfileparser - withName: 'NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER' { + withName: 'BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER' { publishDir = [path: { "${params.outdir}/${task.process.tokenize(':')[-1].toLowerCase()}" }, pattern: "*.log" ] } From f22673482633e6855bf1061df265ba7ed58dcb3f Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 20 Dec 2024 17:33:44 +0000 Subject: [PATCH 06/11] template 3.1.0 update --- .github/ISSUE_TEMPLATE/bug_report.yml | 3 ++- .prettierignore | 1 - 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index b8f3a354..36af0824 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -8,7 +8,8 @@ body: Before you post this issue, please check the documentation: - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - - [bigbio/quantms pipeline documentation](https://nf-co.re/quantms/usage) + - [nf-core/quantms pipeline documentation](https://github.com/bigbio/quantms/usage) + - type: textarea id: description attributes: diff --git a/.prettierignore b/.prettierignore index 9e215fc6..edd29f01 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,5 +10,4 @@ testing/ testing* *.pyc bin/ -venv/ ro-crate-metadata.json From a2e4a6650b3136039b4ceadd027efcc5a23f2195 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 20 Dec 2024 17:34:17 +0000 Subject: [PATCH 07/11] template 3.1.0 update --- .github/ISSUE_TEMPLATE/bug_report.yml | 8 -------- assets/email_template.txt | 8 -------- 2 files changed, 16 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 36af0824..2c821db4 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -2,14 +2,6 @@ name: Bug report description: Report something that is broken or incorrect labels: bug body: - - type: markdown - attributes: - value: | - Before you post this issue, please check the documentation: - - - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - - [nf-core/quantms pipeline documentation](https://github.com/bigbio/quantms/usage) - - type: textarea id: description attributes: diff --git a/assets/email_template.txt b/assets/email_template.txt index 451dfacb..c51ef8a2 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -1,11 +1,3 @@ ----------------------------------------------------- - ,--./,-. - ___ __ __ __ ___ /,-._.--~\\ - |\\ | |__ __ / ` / \\ |__) |__ } { - | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-, - `._,._,' - bigbio/quantms ${version} ----------------------------------------------------- Run Name: $runName <% if (success){ From b45716a650e07af22feb3fa287f52335a2c55c3d Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 20 Dec 2024 17:37:55 +0000 Subject: [PATCH 08/11] ProteinInference new parameter. --- modules/local/openms/proteininference/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/local/openms/proteininference/main.nf b/modules/local/openms/proteininference/main.nf index 8d05ec6a..8dd789a5 100644 --- a/modules/local/openms/proteininference/main.nf +++ b/modules/local/openms/proteininference/main.nf @@ -29,6 +29,7 @@ process PROTEININFERENCE { -protein_fdr true \\ -Algorithm:use_shared_peptides $params.use_shared_peptides \\ -Algorithm:annotate_indistinguishable_groups $groups \\ + -Algorithm:score_type "PEP" \\ $gg \\ -Algorithm:score_aggregation_method $params.protein_score \\ -Algorithm:min_peptides_per_protein $params.min_peptides_per_protein \\ From 054d90637464b0a48e6182232b955cf55734b2e5 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 20 Dec 2024 20:55:22 +0000 Subject: [PATCH 09/11] Make DIANN to mzTab optional --- modules/local/add_sage_feat/main.nf | 6 +++--- modules/local/diannconvert/main.nf | 8 +++++--- modules/local/extract_psm/main.nf | 6 +++--- modules/local/extract_sample/main.nf | 6 +++--- modules/local/generate_diann_cfg/main.nf | 6 +++--- modules/local/mzmlstatistics/main.nf | 6 +++--- modules/local/preprocess_expdesign.nf | 6 +++--- modules/local/samplesheet_check.nf | 6 +++--- modules/local/sdrfparsing/main.nf | 6 +++--- modules/local/spectrum2features/main.nf | 6 +++--- nextflow.config | 1 + nextflow_schema.json | 6 ++++++ 12 files changed, 39 insertions(+), 30 deletions(-) diff --git a/modules/local/add_sage_feat/main.nf b/modules/local/add_sage_feat/main.nf index fee0b605..af27c0ee 100644 --- a/modules/local/add_sage_feat/main.nf +++ b/modules/local/add_sage_feat/main.nf @@ -2,10 +2,10 @@ process SAGEFEATURE { tag "$meta.mzml_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: tuple val(meta), path(id_file), path(extra_feat) diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf index ae7582bf..39968fdb 100644 --- a/modules/local/diannconvert/main.nf +++ b/modules/local/diannconvert/main.nf @@ -2,10 +2,10 @@ process DIANNCONVERT { tag "$meta.experiment_id" label 'process_medium' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: path(report) @@ -31,6 +31,7 @@ process DIANNCONVERT { def args = task.ext.args ?: '' def dia_params = [meta.fragmentmasstolerance,meta.fragmentmasstoleranceunit,meta.precursormasstolerance, meta.precursormasstoleranceunit,meta.enzyme,meta.fixedmodifications,meta.variablemodifications].join(';') + def diann2mztab = params.enable_diann_mztab ? "--enable_diann2mztab" : "" """ quantmsutilsc diann2mztab \\ @@ -41,6 +42,7 @@ process DIANNCONVERT { --charge $params.max_precursor_charge \\ --missed_cleavages $params.allowed_missed_cleavages \\ --qvalue_threshold $params.protein_level_fdr_cutoff \\ + ${diann2mztab} \\ 2>&1 | tee convert_report.log cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/extract_psm/main.nf b/modules/local/extract_psm/main.nf index 93974a09..02c3a6bd 100644 --- a/modules/local/extract_psm/main.nf +++ b/modules/local/extract_psm/main.nf @@ -2,10 +2,10 @@ process PSMCONVERSION { tag "$meta.mzml_id" label 'process_medium' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: diff --git a/modules/local/extract_sample/main.nf b/modules/local/extract_sample/main.nf index d470eb7b..34a602b7 100644 --- a/modules/local/extract_sample/main.nf +++ b/modules/local/extract_sample/main.nf @@ -2,10 +2,10 @@ process GETSAMPLE { tag "$design.Name" label 'process_low' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf index 81e357af..f2fd4d3f 100644 --- a/modules/local/generate_diann_cfg/main.nf +++ b/modules/local/generate_diann_cfg/main.nf @@ -2,10 +2,10 @@ process GENERATE_DIANN_CFG { tag "$meta.experiment_id" label 'process_tiny' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: val(meta) diff --git a/modules/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf index 3ff11be9..d2845e6c 100644 --- a/modules/local/mzmlstatistics/main.nf +++ b/modules/local/mzmlstatistics/main.nf @@ -3,10 +3,10 @@ process MZMLSTATISTICS { label 'process_very_low' label 'process_single' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: tuple val(meta), path(ms_file) diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf index e64549a0..b41d9a80 100644 --- a/modules/local/preprocess_expdesign.nf +++ b/modules/local/preprocess_expdesign.nf @@ -6,10 +6,10 @@ process PREPROCESS_EXPDESIGN { tag "$design.Name" label 'process_tiny' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: path design diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 76b16613..5d767ac9 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK { tag "$input_file" label 'process_tiny' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: path input_file diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf index b3eee998..0c9bf291 100644 --- a/modules/local/sdrfparsing/main.nf +++ b/modules/local/sdrfparsing/main.nf @@ -2,10 +2,10 @@ process SDRFPARSING { tag "$sdrf.Name" label 'process_tiny' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: path sdrf diff --git a/modules/local/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf index 3525c3e2..eda98d8a 100644 --- a/modules/local/spectrum2features/main.nf +++ b/modules/local/spectrum2features/main.nf @@ -2,10 +2,10 @@ process SPECTRUM2FEATURES { tag "$meta.mzml_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: tuple val(meta), path(id_file), path(ms_file) diff --git a/nextflow.config b/nextflow.config index 17fda145..de4d5793 100644 --- a/nextflow.config +++ b/nextflow.config @@ -200,6 +200,7 @@ params { random_preanalysis = false random_preanalysis_seed = 42 empirical_assembly_ms_n = 200 + enable_diann_mztab = true // MSstats general options diff --git a/nextflow_schema.json b/nextflow_schema.json index 770c64c8..9087b38d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1078,6 +1078,12 @@ "default": 200, "fa_icon": "fas fa-filter", "hidden": true + }, + "enable_diann_mztab": { + "type": "boolean", + "description": "Export the DIA-NN and DIA results to mzTab", + "default": true, + "fa_icon": "far fa-check-square" } }, "fa_icon": "fas fa-braille" From 012c54f245d1a506933eb47d2ce6afc91007dfee Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Mon, 23 Dec 2024 07:54:12 +0000 Subject: [PATCH 10/11] Make DIANN to mzTab optional --- modules/local/ms2rescore/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/ms2rescore/main.nf b/modules/local/ms2rescore/main.nf index a8420356..ef492f07 100644 --- a/modules/local/ms2rescore/main.nf +++ b/modules/local/ms2rescore/main.nf @@ -2,10 +2,10 @@ process MS2RESCORE { tag "$meta.mzml_id" label 'process_high' - conda "bioconda::quantms-rescoring=0.0.2" + conda "bioconda::quantms-rescoring=0.0.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-rescoring:0.0.2--pyhdfd78af_0' : - 'biocontainers/quantms-rescoring:0.0.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-rescoring:0.0.3--pyhdfd78af_0' : + 'biocontainers/quantms-rescoring:0.0.3--pyhdfd78af_0' }" // userEmulation settings when docker is specified containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : '' From eed4670e2b680d02f1b8602982ad89a31a271fac Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 20 Dec 2024 17:19:24 +0000 Subject: [PATCH 11/11] Make DIANN to mzTab optional, template 3.1.0, bug fixing --- .github/ISSUE_TEMPLATE/bug_report.yml | 7 ------- .prettierignore | 1 - assets/email_template.txt | 8 -------- conf/modules.config | 4 ++-- conf/test_dia.config | 2 +- conf/test_latest_dia.config | 2 +- modules/local/add_sage_feat/main.nf | 6 +++--- modules/local/diannconvert/main.nf | 8 +++++--- modules/local/extract_psm/main.nf | 6 +++--- modules/local/extract_sample/main.nf | 6 +++--- modules/local/generate_diann_cfg/main.nf | 6 +++--- modules/local/ms2rescore/main.nf | 6 +++--- modules/local/mzmlstatistics/main.nf | 6 +++--- modules/local/openms/proteininference/main.nf | 1 + modules/local/preprocess_expdesign.nf | 6 +++--- modules/local/samplesheet_check.nf | 6 +++--- modules/local/sdrfparsing/main.nf | 6 +++--- modules/local/spectrum2features/main.nf | 6 +++--- nextflow.config | 1 + nextflow_schema.json | 6 ++++++ 20 files changed, 47 insertions(+), 53 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index b8f3a354..2c821db4 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -2,13 +2,6 @@ name: Bug report description: Report something that is broken or incorrect labels: bug body: - - type: markdown - attributes: - value: | - Before you post this issue, please check the documentation: - - - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - - [bigbio/quantms pipeline documentation](https://nf-co.re/quantms/usage) - type: textarea id: description attributes: diff --git a/.prettierignore b/.prettierignore index 9e215fc6..edd29f01 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,5 +10,4 @@ testing/ testing* *.pyc bin/ -venv/ ro-crate-metadata.json diff --git a/assets/email_template.txt b/assets/email_template.txt index 451dfacb..c51ef8a2 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -1,11 +1,3 @@ ----------------------------------------------------- - ,--./,-. - ___ __ __ __ ___ /,-._.--~\\ - |\\ | |__ __ / ` / \\ |__) |__ } { - | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-, - `._,._,' - bigbio/quantms ${version} ----------------------------------------------------- Run Name: $runName <% if (success){ diff --git a/conf/modules.config b/conf/modules.config index 9cb01f92..f2a4f287 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -20,7 +20,7 @@ process { // Local Subworkflows // INPUT_CHECK - withName: 'NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK' { + withName: 'BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK' { publishDir = [ path: { "${params.outdir}/pipeline_info" }, mode: 'copy', @@ -28,7 +28,7 @@ process { ] } - withName: 'NFCORE_QUANTMS:QUANTMS:CUSTOM_DUMPSOFTWAREVERSIONS' { + withName: 'BIGBIO_QUANTMS:QUANTMS:CUSTOM_DUMPSOFTWAREVERSIONS' { publishDir = [ path: { "${params.outdir}/pipeline_info" }, mode: params.publish_dir_mode, diff --git a/conf/test_dia.config b/conf/test_dia.config index 2bd1510b..5f90dfc0 100644 --- a/conf/test_dia.config +++ b/conf/test_dia.config @@ -42,7 +42,7 @@ params { process { // thermorawfileparser - withName: 'NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER' { + withName: 'BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER' { publishDir = [path: { "${params.outdir}/${task.process.tokenize(':')[-1].toLowerCase()}" }, pattern: "*.log" ] } } diff --git a/conf/test_latest_dia.config b/conf/test_latest_dia.config index f7c047f2..72dad9dc 100644 --- a/conf/test_latest_dia.config +++ b/conf/test_latest_dia.config @@ -35,7 +35,7 @@ params { process { // thermorawfileparser - withName: 'NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER' { + withName: 'BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER' { publishDir = [path: { "${params.outdir}/${task.process.tokenize(':')[-1].toLowerCase()}" }, pattern: "*.log" ] } diff --git a/modules/local/add_sage_feat/main.nf b/modules/local/add_sage_feat/main.nf index fee0b605..af27c0ee 100644 --- a/modules/local/add_sage_feat/main.nf +++ b/modules/local/add_sage_feat/main.nf @@ -2,10 +2,10 @@ process SAGEFEATURE { tag "$meta.mzml_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: tuple val(meta), path(id_file), path(extra_feat) diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf index ae7582bf..39968fdb 100644 --- a/modules/local/diannconvert/main.nf +++ b/modules/local/diannconvert/main.nf @@ -2,10 +2,10 @@ process DIANNCONVERT { tag "$meta.experiment_id" label 'process_medium' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: path(report) @@ -31,6 +31,7 @@ process DIANNCONVERT { def args = task.ext.args ?: '' def dia_params = [meta.fragmentmasstolerance,meta.fragmentmasstoleranceunit,meta.precursormasstolerance, meta.precursormasstoleranceunit,meta.enzyme,meta.fixedmodifications,meta.variablemodifications].join(';') + def diann2mztab = params.enable_diann_mztab ? "--enable_diann2mztab" : "" """ quantmsutilsc diann2mztab \\ @@ -41,6 +42,7 @@ process DIANNCONVERT { --charge $params.max_precursor_charge \\ --missed_cleavages $params.allowed_missed_cleavages \\ --qvalue_threshold $params.protein_level_fdr_cutoff \\ + ${diann2mztab} \\ 2>&1 | tee convert_report.log cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/extract_psm/main.nf b/modules/local/extract_psm/main.nf index 93974a09..02c3a6bd 100644 --- a/modules/local/extract_psm/main.nf +++ b/modules/local/extract_psm/main.nf @@ -2,10 +2,10 @@ process PSMCONVERSION { tag "$meta.mzml_id" label 'process_medium' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: diff --git a/modules/local/extract_sample/main.nf b/modules/local/extract_sample/main.nf index d470eb7b..34a602b7 100644 --- a/modules/local/extract_sample/main.nf +++ b/modules/local/extract_sample/main.nf @@ -2,10 +2,10 @@ process GETSAMPLE { tag "$design.Name" label 'process_low' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf index 81e357af..f2fd4d3f 100644 --- a/modules/local/generate_diann_cfg/main.nf +++ b/modules/local/generate_diann_cfg/main.nf @@ -2,10 +2,10 @@ process GENERATE_DIANN_CFG { tag "$meta.experiment_id" label 'process_tiny' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: val(meta) diff --git a/modules/local/ms2rescore/main.nf b/modules/local/ms2rescore/main.nf index a8420356..ef492f07 100644 --- a/modules/local/ms2rescore/main.nf +++ b/modules/local/ms2rescore/main.nf @@ -2,10 +2,10 @@ process MS2RESCORE { tag "$meta.mzml_id" label 'process_high' - conda "bioconda::quantms-rescoring=0.0.2" + conda "bioconda::quantms-rescoring=0.0.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-rescoring:0.0.2--pyhdfd78af_0' : - 'biocontainers/quantms-rescoring:0.0.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-rescoring:0.0.3--pyhdfd78af_0' : + 'biocontainers/quantms-rescoring:0.0.3--pyhdfd78af_0' }" // userEmulation settings when docker is specified containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : '' diff --git a/modules/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf index 3ff11be9..d2845e6c 100644 --- a/modules/local/mzmlstatistics/main.nf +++ b/modules/local/mzmlstatistics/main.nf @@ -3,10 +3,10 @@ process MZMLSTATISTICS { label 'process_very_low' label 'process_single' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: tuple val(meta), path(ms_file) diff --git a/modules/local/openms/proteininference/main.nf b/modules/local/openms/proteininference/main.nf index 8d05ec6a..8dd789a5 100644 --- a/modules/local/openms/proteininference/main.nf +++ b/modules/local/openms/proteininference/main.nf @@ -29,6 +29,7 @@ process PROTEININFERENCE { -protein_fdr true \\ -Algorithm:use_shared_peptides $params.use_shared_peptides \\ -Algorithm:annotate_indistinguishable_groups $groups \\ + -Algorithm:score_type "PEP" \\ $gg \\ -Algorithm:score_aggregation_method $params.protein_score \\ -Algorithm:min_peptides_per_protein $params.min_peptides_per_protein \\ diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf index e64549a0..b41d9a80 100644 --- a/modules/local/preprocess_expdesign.nf +++ b/modules/local/preprocess_expdesign.nf @@ -6,10 +6,10 @@ process PREPROCESS_EXPDESIGN { tag "$design.Name" label 'process_tiny' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: path design diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 76b16613..5d767ac9 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK { tag "$input_file" label 'process_tiny' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: path input_file diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf index b3eee998..0c9bf291 100644 --- a/modules/local/sdrfparsing/main.nf +++ b/modules/local/sdrfparsing/main.nf @@ -2,10 +2,10 @@ process SDRFPARSING { tag "$sdrf.Name" label 'process_tiny' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: path sdrf diff --git a/modules/local/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf index 3525c3e2..eda98d8a 100644 --- a/modules/local/spectrum2features/main.nf +++ b/modules/local/spectrum2features/main.nf @@ -2,10 +2,10 @@ process SPECTRUM2FEATURES { tag "$meta.mzml_id" label 'process_low' - conda "bioconda::quantms-utils=0.0.17" + conda "bioconda::quantms-utils=0.0.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' : - 'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.18--pyh7e72e81_0' : + 'biocontainers/quantms-utils:0.0.18--pyh7e72e81_0' }" input: tuple val(meta), path(id_file), path(ms_file) diff --git a/nextflow.config b/nextflow.config index 17fda145..de4d5793 100644 --- a/nextflow.config +++ b/nextflow.config @@ -200,6 +200,7 @@ params { random_preanalysis = false random_preanalysis_seed = 42 empirical_assembly_ms_n = 200 + enable_diann_mztab = true // MSstats general options diff --git a/nextflow_schema.json b/nextflow_schema.json index 770c64c8..9087b38d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1078,6 +1078,12 @@ "default": 200, "fa_icon": "fas fa-filter", "hidden": true + }, + "enable_diann_mztab": { + "type": "boolean", + "description": "Export the DIA-NN and DIA results to mzTab", + "default": true, + "fa_icon": "far fa-check-square" } }, "fa_icon": "fas fa-braille"