From ff70a590dd4ef434f99c8c0eab0e1fcabb671099 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Tue, 7 Jan 2025 14:55:20 +0100 Subject: [PATCH 1/5] Template update for nf-core/tools version 3.1.1 --- .github/workflows/download_pipeline.yml | 29 +++++++++++-------------- .github/workflows/linting_comment.yml | 2 +- .nf-core.yml | 2 +- README.md | 2 +- 4 files changed, 16 insertions(+), 19 deletions(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 977b425..ce81c33 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -29,22 +29,11 @@ env: jobs: configure: - runs-on: ubuntu-latest{% raw %} + 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: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }} - steps: - - name: Get the repository name and current branch - id: get_repo_properties - run: | - echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" - echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT{% endraw %}" - - download: - runs-on: ubuntu-latest - needs: configure steps: - name: Install Nextflow uses: nf-core/setup-nextflow@v2 @@ -67,10 +56,21 @@ jobs: python -m pip install --upgrade pip 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_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{% raw %} @@ -85,10 +85,7 @@ jobs: --download-configuration 'yes' - name: Inspect download - run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %} - - - name: Inspect container images - run: tree ./singularity_container_images | tee ./container_initial{% if test_config %}{% raw %} + run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} - name: Count the downloaded number of container images id: count_initial diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 95b6b6a..0bed96d 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8 + uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.nf-core.yml b/.nf-core.yml index ced508b..9798bd5 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -27,7 +27,7 @@ lint: nextflow_config: - manifest.name - manifest.homePage -nf_core_version: 3.2.0 +nf_core_version: 3.1.1 repository_type: pipeline template: author: SusiJo, FriederikeHanssen, famosab diff --git a/README.md b/README.md index e93e829..25f5e14 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ The resulting file(s) can be analyzed singly or as an entire cohort in R with [m ## 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. First, prepare a samplesheet with your input data that looks as follows: From 0e9046e248b0292206f126c40c9d69b46edda3cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Tue, 6 May 2025 16:21:28 +0200 Subject: [PATCH 2/5] template update --- .github/workflows/download_pipeline.yml | 25 ++++++++++++++----------- .github/workflows/linting_comment.yml | 2 +- .nf-core.yml | 2 +- README.md | 2 +- docs/output.md | 4 +++- 5 files changed, 20 insertions(+), 15 deletions(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index ce81c33..f60afc0 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -34,6 +34,17 @@ jobs: REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }} + steps: + - name: Get the repository name and current branch + id: get_repo_properties + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" + + download: + runs-on: ubuntu-latest + needs: configure steps: - name: Install Nextflow uses: nf-core/setup-nextflow@v2 @@ -56,21 +67,10 @@ jobs: python -m pip install --upgrade pip 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_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{% raw %} @@ -87,6 +87,9 @@ jobs: - name: Inspect download run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} + - name: Inspect container images + run: tree ./singularity_container_images | tee ./container_initial + - name: Count the downloaded number of container images id: count_initial run: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 0bed96d..95b6b6a 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7 + uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.nf-core.yml b/.nf-core.yml index 9798bd5..ced508b 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -27,7 +27,7 @@ lint: nextflow_config: - manifest.name - manifest.homePage -nf_core_version: 3.1.1 +nf_core_version: 3.2.0 repository_type: pipeline template: author: SusiJo, FriederikeHanssen, famosab diff --git a/README.md b/README.md index 25f5e14..e93e829 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ The resulting file(s) can be analyzed singly or as an entire cohort in R with [m ## 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. First, prepare a samplesheet with your input data that looks as follows: diff --git a/docs/output.md b/docs/output.md index 88d7720..630436b 100644 --- a/docs/output.md +++ b/docs/output.md @@ -70,7 +70,9 @@ 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 From fb320070ca9de9e5c3926972fac2bab277bc9558 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Tue, 6 May 2025 16:15:17 +0200 Subject: [PATCH 3/5] Template update for nf-core/tools version 3.2.1 --- .nf-core.yml | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index ced508b..b4a8033 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -27,7 +27,7 @@ lint: nextflow_config: - manifest.name - manifest.homePage -nf_core_version: 3.2.0 +nf_core_version: 3.2.1 repository_type: pipeline template: author: SusiJo, FriederikeHanssen, famosab diff --git a/nextflow.config b/nextflow.config index 81813de..19f6d00 100644 --- a/nextflow.config +++ b/nextflow.config @@ -264,7 +264,7 @@ manifest { // Nextflow plugins plugins { - id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { From f9c544c9bdeec11cc48432ca966abeaadcaff07d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Tue, 6 May 2025 16:23:22 +0200 Subject: [PATCH 4/5] changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 45ddec4..ed13346 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#34](https://github.com/qbic-pipelines/vcftomaf/pull/34) - Update vcf2maf configuration to adhere to hg38 as reference genome (@famosab) - [#35](https://github.com/qbic-pipelines/vcftomaf/pull/35) - Template update to 3.2.0 (@famosab) +- [#37](https://github.com/qbic-pipelines/vcftomaf/pull/37) - Template update to 3.2.1 (@famosab) + ### `Dependencies` From 59af64c5bb1b8ca2ffc8c3bbe473df19f78994d0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Tue, 6 May 2025 16:24:39 +0200 Subject: [PATCH 5/5] changelog prettier --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ed13346..23e2e8c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#35](https://github.com/qbic-pipelines/vcftomaf/pull/35) - Template update to 3.2.0 (@famosab) - [#37](https://github.com/qbic-pipelines/vcftomaf/pull/37) - Template update to 3.2.1 (@famosab) - ### `Dependencies` | Dependency | Old version | New version |