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Merge pull request #1484 from nf-core/dev
Release 3.4.2
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‎.github/workflows/ci.yml

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- tags: "tabix/tabix"
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- tags: "tiddit/sv"
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- tags: "untar"
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- tags: "pipeline_sarek"
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include:
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- tags: "pipeline_sarek"
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profile: "test,docker"
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env:
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NXF_ANSI_LOG: false
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TEST_DATA_BASE: "${{ github.workspace }}/test-datasets"

‎.github/workflows/cloudtest.yml

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default: true
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jobs:
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trigger-profile-test:
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name: Run AWS tests
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trigger-test:
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name: launch
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runs-on: ubuntu-latest
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if: ${{ github.repository == 'nf-core/sarek' }}
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strategy:
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fail-fast: false
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matrix:
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include:
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- profile: test_aws
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enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.test && inputs.aws ) ) }}
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test: test
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cloud: aws
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compute_env: TOWER_COMPUTE_ENV
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workdir: TOWER_BUCKET_AWS
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- profile: test_azure
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enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.test && inputs.azure ) ) }}
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test: test
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cloud: azure
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compute_env: TOWER_CE_AZURE_CPU
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workdir: TOWER_BUCKET_AZURE
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- profile: test_full_aws
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enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.somatic && inputs.aws ) ) }}
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test: somatic
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cloud: aws
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compute_env: TOWER_COMPUTE_ENV
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workdir: TOWER_BUCKET_AWS
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- profile: test_full_azure
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enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.somatic && inputs.azure ) ) }}
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test: somatic
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cloud: azure
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compute_env: TOWER_CE_AZURE_CPU
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workdir: TOWER_BUCKET_AZURE
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- profile: test_full_germline_aws
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enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.aws ) ) }}
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test: germline
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cloud: aws
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compute_env: TOWER_COMPUTE_ENV
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workdir: TOWER_BUCKET_AWS
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- profile: test_full_germline_azure
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enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.azure ) ) }}
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- profile: test_full_germline_ncbench_agilent_aws
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enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline_ncbench_agilent && inputs.aws ) ) }}
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test: germline
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cloud: azure
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compute_env: TOWER_CE_AZURE_CPU
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workdir: TOWER_BUCKET_AZURE
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- profile: test_full_germline_ncbench_agilent
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test: germline_ncbench_agilent
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cloud: aws
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compute_env: TOWER_COMPUTE_ENV
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workdir: TOWER_BUCKET_AWS
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steps:
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# Launch workflow on AWS Batch
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- name: AWS Launch
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- name: Launch
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uses: seqeralabs/action-tower-launch@v2
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if: ${{ matrix.enabled && ( github.event_name != 'workflow_dispatch' || inputs.aws ) }}
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# If inputs item exists (i.e. workflow_dispatch), then we find matrix.test and check it is false
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# If is false, we negate and run the job
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if: ( !contains(inputs[matrix.test], 'false') && !contains(inputs[matrix.cloud], 'false') )
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with:
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run_name: sarek_${{ matrix.profile }}
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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compute_env: ${{ secrets[matrix.compute_env] }}
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revision: ${{ github.sha }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/${{ matrix.profile }}
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workdir: ${{ secrets[matrix.workdir] }}/work/sarek/work-${{ github.sha }}/${{ matrix.profile }}
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/"
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"outdir": "${{ secrets[matrix.workdir] }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/"
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}
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profiles: ${{ matrix.profile }}
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- uses: actions/upload-artifact@v3
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name: Save AWS Logs
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name: Save Logs
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if: success() || failure()
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with:
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name: tower-aws-${{ matrix.profile }}-log
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path: |
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tower_action_*.log
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tower_action_*.json
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# Launch workflow using Tower CLI tool action
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- name: Azure Launch
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uses: seqeralabs/action-tower-launch@v2
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if: ${{ matrix.enabled && ( github.event_name != 'workflow_dispatch' || inputs.azure ) }}
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with:
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run_name: sarek_${{ matrix.profile }}
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
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revision: ${{ github.sha }}
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workdir: ${{ secrets.TOWER_BUCKET_AZURE}}/sarek/work-${{ github.sha }}/${{ matrix.profile }}
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/"
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}
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profiles: ${{ matrix.profile }}
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- uses: actions/upload-artifact@v3
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name: Save Azure Logs
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if: success() || failure()
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with:
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name: tower-azure-${{ matrix.profile }}-log
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name: tower-${{ matrix.profile }}-log
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path: |
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tower_action_*.log
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tower_action_*.json

‎CHANGELOG.md

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@@ -5,6 +5,52 @@ All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [3.4.2](https://github.com/nf-core/sarek/releases/tag/3.4.2) - Sájtáristjåhkkå
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Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is one of the few peaks in Sweden that cannot be climbed without proper climbing equipment.
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### Added
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- [#1489](https://github.com/nf-core/sarek/pull/1489) - Added a `testdata.nf-core.sarek` key in `conf/igenomes.config` for small reference
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- [#1493](https://github.com/nf-core/sarek/pull/1493) - Added a `wave` profile
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- [#1498](https://github.com/nf-core/sarek/pull/1498) - Prepare release `3.4.2`
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### Changed
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- [#1477](https://github.com/nf-core/sarek/pull/1477) - Back to dev
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- [#1482](https://github.com/nf-core/sarek/pull/1482) - Pin `nf-prov` plugin to `1.2.2`
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- [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication
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- [#1487](https://github.com/nf-core/sarek/pull/1487) - Update sentieon-modules to Sentieon `202308.02`
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- [#1490](https://github.com/nf-core/sarek/pull/1490) - Update mosdepth to `0.3.8`
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- [#1505](https://github.com/nf-core/sarek/pull/1505) - Update CITATIONS.md
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- [#1506](https://github.com/nf-core/sarek/pull/1506) - Fixing typos (`index_alignement` -> `index_alignment`)
27+
- [#1509](https://github.com/nf-core/sarek/pull/1509) - Update contributors
28+
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### Fixed
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- [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix
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- [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline`
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- [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix Cloud Storage objects are immutable on GCP [#1491](https://github.com/nf-core/sarek/issues/1491)
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- [#1496](https://github.com/nf-core/sarek/pull/1496) - Fix multiple DOI handling in manifest
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- [#1499](https://github.com/nf-core/sarek/pull/1499) - Remove all md5sum for mosdepth tests
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- [#1499](https://github.com/nf-core/sarek/pull/1499) - Add mosdepth dependency to all tests runnning it
37+
- [#1501](https://github.com/nf-core/sarek/pull/1501) - Remove string "None" param option from ascat_genome
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### Removed
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- [#1489](https://github.com/nf-core/sarek/pull/1489) - Remove `test_cache` profile
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### Dependencies
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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| `mosdepth` | 0.3.6 | 0.3.8 |
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| `sentieon` | 202308.01 | 202308.02 |
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### Modules / Subworkflows
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### Parameters
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## [3.4.1](https://github.com/nf-core/sarek/releases/tag/3.4.1) - Balgattjåhkkå
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Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the other one being Pårtetjåkko (Bårddetjåhkkå).
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### Dependencies
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
76-
| bcftools | 1.17 | 1.18 |
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| ensemblvep | 110.0 | 111.0 |
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| fgbio | 2.0.2 | 2.1.0 |
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| gatk | 4.4.0.0 | 4.5.0.0 |
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| gatk-spark | 4.4.0.0 | 4.5.0.0 |
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| mosdepth | 0.3.3 | 0.3.6 |
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| multiqc | 1.17 | 1.18 |
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| samtools | 1.17 | 1.19.2 |
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| Dependency | Old version | New version |
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| ------------ | ----------- | ----------- |
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| `bcftools` | 1.17 | 1.18 |
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| `ensemblvep` | 110.0 | 111.0 |
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| `fgbio` | 2.0.2 | 2.1.0 |
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| `gatk` | 4.4.0.0 | 4.5.0.0 |
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| `gatk-spark` | 4.4.0.0 | 4.5.0.0 |
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| `mosdepth` | 0.3.3 | 0.3.6 |
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| `multiqc` | 1.17 | 1.18 |
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| `samtools` | 1.17 | 1.19.2 |
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### Modules / Subworkflows
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### Parameter
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| Old name | New name |
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| -------------------------- | ------------------------ |
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| bcftools_annotations_index | bcftools_annotations_tbi |
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| Old name | New name |
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| ---------------------------- | -------------------------- |
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| `bcftools_annotations_index` | `bcftools_annotations_tbi` |
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## [3.4.0](https://github.com/nf-core/sarek/releases/tag/3.4.0) - Pårtetjåkko
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| Dependency | Old version | New version |
143189
| ---------- | ----------- | ----------- |
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| fastqc | 0.11.9 | 0.12.1 |
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| multiqc | 1.15 | 1.17 |
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| `fastqc` | 0.11.9 | 0.12.1 |
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| `multiqc` | 1.15 | 1.17 |
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### Modules / Subworkflows
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### Dependencies
177223

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| Dependency | Old version | New version |
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| -------------------------------- | ----------- | ----------- |
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| Control-FREEC/assesssignificance | 11.6b | 11.6 |
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| Dependency | Old version | New version |
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| ---------------------------------- | ----------- | ----------- |
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| `Control-FREEC/assesssignificance` | 11.6b | 11.6 |
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## [3.3.1](https://github.com/nf-core/sarek/releases/tag/3.3.1) - Biellorippjávrre
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### Dependencies
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| Dependency | Old version | New version |
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| ------------- | ----------- | ----------- |
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| Control-FREEC | 11.6 | 11.6b |
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| Dependency | Old version | New version |
251+
| --------------- | ----------- | ----------- |
252+
| `Control-FREEC` | 11.6 | 11.6b |
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## [3.3.0](https://github.com/nf-core/sarek/releases/tag/3.3.0) - Rapaselet
209255

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### Fixed
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- [#1087](https://github.com/nf-core/sarek/pull/1087) - Fix wrong default memory in GATK4_CREATESEQUENCEDICTIONARY [#1085](https://github.com/nf-core/sarek/pull/1085)
369+
- [#1087](https://github.com/nf-core/sarek/pull/1087) - Fix wrong default memory in `GATK4_CREATESEQUENCEDICTIONARY` [#1085](https://github.com/nf-core/sarek/pull/1085)
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- [#1089](https://github.com/nf-core/sarek/pull/1089) - Remove duplicated code
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- [#1093](https://github.com/nf-core/sarek/pull/1093) - Fixing Ascat by reverting meta.id in channels allele_files, loci_files, gc_file and rt_file to baseName
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- [#1098](https://github.com/nf-core/sarek/pull/1098) - Fix Channel issue in Mutect2 subworkflow [#1094](https://github.com/nf-core/sarek/pull/1094)

‎CITATIONS.md

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- [FGBio](https://github.com/fulcrumgenomics/fgbio)
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> doi: 10.5281/zenodo.10456900
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- [FreeBayes](https://arxiv.org/abs/1207.3907)
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> Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012. doi: 10.48550/arXiv.1207.3907

‎README.md

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@@ -153,13 +153,15 @@ We thank the following people for their extensive assistance in the development
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- [Johannes Alneberg](https://github.com/alneberg)
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- [José Fernández Navarro](https://github.com/jfnavarro)
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- [Júlia Mir Pedrol](https://github.com/mirpedrol)
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- [Ken Brewer](https://github.com/kenibrewer)
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- [Lasse Westergaard Folkersen](https://github.com/lassefolkersen)
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- [Lucia Conde](https://github.com/lconde-ucl)
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- [Malin Larsson](https://github.com/malinlarsson)
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- [Marcel Martin](https://github.com/marcelm)
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- [Nick Smith](https://github.com/nickhsmith)
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- [Nicolas Schcolnicov](https://github.com/nschcolnicov)
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- [Nilesh Tawari](https://github.com/nilesh-tawari)
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- [Nils Homer](https://github.com/nh13)
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- [Olga Botvinnik](https://github.com/olgabot)
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- [Oskar Wacker](https://github.com/WackerO)
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- [pallolason](https://github.com/pallolason)
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- [Sam Minot](https://github.com/sminot)
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- [Sebastian-D](https://github.com/Sebastian-D)
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- [Silvia Morini](https://github.com/silviamorins)
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- [Simon Pearce](https://github.com/SPPearce)
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- [Solenne Correard](https://github.com/scorreard)
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- [Susanne Jodoin](https://github.com/SusiJo)
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- [Szilveszter Juhos](https://github.com/szilvajuhos)
@@ -193,7 +196,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
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If you use `nf-core/sarek` for your analysis, please cite the `Sarek` article as follows:
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> Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen **Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery** _bioRxiv_ [doi: 10.1101/2023.07.19.549462](https://doi.org/10.1101/2023.07.19.549462).
199+
> Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen **Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery** _NAR Genomics and Bioinformatics_ Volume 6, Issue 2, June 2024, lqae031, [doi: 10.1093/nargab/lqae031](https://doi.org/10.1093/nargab/lqae031).
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> Garcia M, Juhos S, Larsson M et al. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]** _F1000Research_ 2020, 9:63 [doi: 10.12688/f1000research.16665.2](http://dx.doi.org/10.12688/f1000research.16665.2).
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‎assets/multiqc_config.yml

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custom_logo_title: "nf-core/sarek"
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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/3.4.1" target="_blank">nf-core/sarek</a>
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This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/3.4.2" target="_blank">nf-core/sarek</a>
77
analysis pipeline. For information about how to interpret these results, please see the
8-
<a href="https://nf-co.re/sarek/3.4.1/docs/output" target="_blank">documentation</a>.
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<a href="https://nf-co.re/sarek/3.4.2/docs/output" target="_blank">documentation</a>.
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report_section_order:
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"nf-core-sarek-methods-description":
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order: -1000

‎conf/igenomes.config

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fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
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readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
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}
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'testdata.nf-core.sarek' {
324+
dbsnp = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
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dbsnp_tbi = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
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dbsnp_vqsr = '--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz'
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dict = "${params.igenomes_base}/genomics/homo_sapiens/genome/genome.dict"
328+
fasta = "${params.igenomes_base}/genomics/homo_sapiens/genome/genome.fasta"
329+
fasta_fai = "${params.igenomes_base}/genomics/homo_sapiens/genome/genome.fasta.fai"
330+
germline_resource = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
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germline_resource_tbi = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi"
332+
intervals = "${params.igenomes_base}/genomics/homo_sapiens/genome/genome.interval_list"
333+
known_indels = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
334+
known_indels_tbi = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
335+
known_indels_vqsr = '--resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz'
336+
ngscheckmate_bed = "${params.igenomes_base}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
337+
snpeff_db = '105'
338+
snpeff_genome = 'WBcel235'
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vep_cache_version = '110'
340+
vep_genome = 'WBcel235'
341+
vep_species = 'caenorhabditis_elegans'
342+
}
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}
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}

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