major change to run CI on dev using dev conf

.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

.github/CONTRIBUTING.md

@@ -1,22 +1,22 @@
-# `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 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).
@@ -65,7 +65,7 @@ For further information/help, please consult the [bigbio/quantms documentation](
 
 ## 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

.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://nf-co.re/quantms/usage)
-
   - type: textarea
     id: description
     attributes:
@@ -47,4 +39,4 @@ 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)_

.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

.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

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,22 +1,22 @@
 <!--
-# nf-core/quantms pull request
+# bigbio/quantms pull request
 
-Many thanks for contributing to nf-core/quantms!
+Many thanks for contributing to bigbio/quantms!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/quantms/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/bigbio/quantms/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## 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 <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

.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

.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

.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
@@ -53,65 +57,70 @@ 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/" \
           --container-cache-utilisation 'amend' \
           --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
         continue-on-error: true
         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

.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.

.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

.prettierignore

@@ -10,5 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
-venv/
-
+ro-crate-metadata.json

CHANGELOG.md

@@ -1,4 +1,4 @@
-# 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).
@@ -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`
 

CITATIONS.md

@@ -1,4 +1,4 @@
-# nf-core/quantms: Citations
+# bigbio/quantms: Citations
 
 ## [Pipeline](https://www.researchsquare.com/article/rs-3002027/v1)
 

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