From 0fd827f29abd3313f172355c412e6a9de0ff7c75 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Fri, 22 Nov 2024 16:35:33 +0100 Subject: [PATCH 1/8] remove download test --- .github/workflows/download_pipeline.yml | 119 ------------------------ 1 file changed, 119 deletions(-) delete mode 100644 .github/workflows/download_pipeline.yml diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml deleted file mode 100644 index 713dc3e..0000000 --- a/.github/workflows/download_pipeline.yml +++ /dev/null @@ -1,119 +0,0 @@ -name: Test successful pipeline download with 'nf-core pipelines download' - -# Run the workflow when: -# - dispatched manually -# - when a PR is opened or reopened to master branch -# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. -on: - workflow_dispatch: - inputs: - testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." - required: true - default: "dev" - pull_request: - types: - - opened - - edited - - synchronize - branches: - - master - pull_request_target: - branches: - - master - -env: - NXF_ANSI_LOG: false - -jobs: - download: - runs-on: ubuntu-latest - steps: - - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 - - - name: Disk space cleanup - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 - with: - python-version: "3.12" - architecture: "x64" - - - name: Setup Apptainer - uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 - with: - apptainer-version: 1.3.4 - - - name: Install dependencies - run: | - 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 - 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} - - - name: Make a cache directory for the container images - run: | - mkdir -p ./singularity_container_images - - - 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 }} \ - --compress "none" \ - --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ - --container-cache-utilisation 'amend' \ - --download-configuration 'yes' - - - name: Inspect download - run: tree ./${{ env.REPOTITLE_LOWERCASE }} - - - name: Count the downloaded number of container images - id: count_initial - run: | - image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) - echo "Initial container image count: $image_count" - echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} - - - name: Run the downloaded pipeline (stub) - id: stub_run_pipeline - continue-on-error: true - env: - NXF_SINGULARITY_CACHEDIR: ./singularity_container_images - NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - - name: Run the downloaded pipeline (stub run not supported) - id: run_pipeline - if: ${{ job.steps.stub_run_pipeline.status == failure() }} - env: - NXF_SINGULARITY_CACHEDIR: ./singularity_container_images - NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results - - - name: Count the downloaded number of container images - id: count_afterwards - run: | - image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) - echo "Post-pipeline run container image count: $image_count" - echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} - - - name: Compare container image counts - run: | - if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then - initial_count=${{ env.IMAGE_COUNT_INITIAL }} - final_count=${{ env.IMAGE_COUNT_AFTER }} - difference=$((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 - exit 1 - else - echo "The pipeline can be downloaded successfully!" - fi From 32b097b9fd422ca08a6539d89570dd6809ae1673 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Fri, 22 Nov 2024 16:36:48 +0100 Subject: [PATCH 2/8] update swbf --- modules.json | 4 ++-- .../tests/main.workflow.nf.test | 10 ++++++---- .../nf-core/utils_nfschema_plugin/tests/main.nf.test | 4 ++-- 3 files changed, 10 insertions(+), 8 deletions(-) diff --git a/modules.json b/modules.json index 1f93311..947bd6e 100644 --- a/modules.json +++ b/modules.json @@ -52,7 +52,7 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", + "git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { @@ -62,7 +62,7 @@ }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", + "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", "installed_by": ["subworkflows"] } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index ca964ce..02dbf09 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -52,10 +52,12 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 842dc43..8fb3016 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -42,7 +42,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { @@ -94,7 +94,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { From ed667679b50d2d0ae72e9416e7102e05956b95d7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Fri, 22 Nov 2024 15:08:11 +0100 Subject: [PATCH 3/8] remove unused module bcftools/concat --- modules.json | 44 ++++++++++++++++++++++++++++++++------------ 1 file changed, 32 insertions(+), 12 deletions(-) diff --git a/modules.json b/modules.json index fed38c0..2ae2011 100644 --- a/modules.json +++ b/modules.json @@ -8,37 +8,51 @@ "bcftools/view": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gunzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "picard/liftovervcf": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcf2maf": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/vcf2maf/vcf2maf.diff" } } @@ -47,18 +61,24 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c", - "installed_by": ["subworkflows"] + "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", - "installed_by": ["subworkflows"] + "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", + "installed_by": [ + "subworkflows" + ] } } } From cb914df39b34e0092b5ee498482e459304dabfc5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Fri, 22 Nov 2024 15:12:03 +0100 Subject: [PATCH 4/8] prettier --- modules.json | 40 ++++++++++------------------------------ 1 file changed, 10 insertions(+), 30 deletions(-) diff --git a/modules.json b/modules.json index 2ae2011..be3070d 100644 --- a/modules.json +++ b/modules.json @@ -8,51 +8,37 @@ "bcftools/view": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gunzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/liftovervcf": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcf2maf": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/vcf2maf/vcf2maf.diff" } } @@ -62,23 +48,17 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } From 61a7230b9a3afb70b12b397807bc8bfa15e55f7d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Mon, 25 Nov 2024 10:05:44 +0100 Subject: [PATCH 5/8] update changelog --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 99001bc..482c592 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.1.0 - 22-11-2024 - Amaranth Filly +## v1.1.0 - 25-11-2024 - Amaranth Filly ### `Added` @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#16](https://github.com/qbic-pipelines/vcftomaf/pull/16) - Template update to 3.0.2 (@famosab) - [#17](https://github.com/qbic-pipelines/vcftomaf/pull/17) - Update all modules (@famosab) +- [#20](https://github.com/qbic-pipelines/vcftomaf/pull/20) - Remove unused CI tests ### `Dependencies` From 516b320d4df71454be08d3ad5a176674013895a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Mon, 25 Nov 2024 10:10:40 +0100 Subject: [PATCH 6/8] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 482c592..3e0be6a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,4 +24,4 @@ Thanks to @d4straub for reviews. ## v1.0.0 - 13-03-2024 - Plum Puppy -Initial release of qbic-pipelines/vcftomaf, created with the [nf-core](https://nf-co.re/) template. +Initial release of qbic-pipelines/vcftomaf, created with the [nf-core](https://nf-co.re/) template, written by @SusiJo and @FriederikeHanssen. From 3e2dae3ba005541c9ec8e6df2ca76d2e9c034c08 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Mon, 25 Nov 2024 10:56:57 +0100 Subject: [PATCH 7/8] add download test back --- .github/workflows/download_pipeline.yml | 119 ++++++++++++++++++++++++ 1 file changed, 119 insertions(+) create mode 100644 .github/workflows/download_pipeline.yml diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml new file mode 100644 index 0000000..713dc3e --- /dev/null +++ b/.github/workflows/download_pipeline.yml @@ -0,0 +1,119 @@ +name: Test successful pipeline download with 'nf-core pipelines download' + +# Run the workflow when: +# - dispatched manually +# - when a PR is opened or reopened to master branch +# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. +on: + workflow_dispatch: + inputs: + testbranch: + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." + required: true + default: "dev" + pull_request: + types: + - opened + - edited + - synchronize + branches: + - master + pull_request_target: + branches: + - master + +env: + NXF_ANSI_LOG: false + +jobs: + download: + runs-on: ubuntu-latest + steps: + - name: Install Nextflow + uses: nf-core/setup-nextflow@v2 + + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + with: + python-version: "3.12" + architecture: "x64" + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 + with: + apptainer-version: 1.3.4 + + - name: Install dependencies + run: | + 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 + 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} + + - name: Make a cache directory for the container images + run: | + mkdir -p ./singularity_container_images + + - 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 }} \ + --compress "none" \ + --container-system 'singularity' \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ + --container-cache-utilisation 'amend' \ + --download-configuration 'yes' + + - name: Inspect download + run: tree ./${{ env.REPOTITLE_LOWERCASE }} + + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + + - name: Run the downloaded pipeline (stub) + id: stub_run_pipeline + continue-on-error: true + env: + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + - name: Run the downloaded pipeline (stub run not supported) + id: run_pipeline + if: ${{ job.steps.stub_run_pipeline.status == failure() }} + env: + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + + - name: Compare container image counts + run: | + if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ env.IMAGE_COUNT_INITIAL }} + final_count=${{ env.IMAGE_COUNT_AFTER }} + difference=$((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 + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi From 1ba51b1149790003a1b1f8dcf1000e6b745989ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Mon, 25 Nov 2024 10:57:52 +0100 Subject: [PATCH 8/8] update Changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e0be6a..f446c10 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#16](https://github.com/qbic-pipelines/vcftomaf/pull/16) - Template update to 3.0.2 (@famosab) - [#17](https://github.com/qbic-pipelines/vcftomaf/pull/17) - Update all modules (@famosab) -- [#20](https://github.com/qbic-pipelines/vcftomaf/pull/20) - Remove unused CI tests +- [#20](https://github.com/qbic-pipelines/vcftomaf/pull/20) - Update subworkflows (@famosab) ### `Dependencies`