diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 8fef331d76..4da19793b1 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -20,9 +20,9 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }} + workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/germline_test parameters: | { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}" + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/germline_test" } profiles: test_full,aws_tower diff --git a/.github/workflows/awsfulltest_somatic.yml b/.github/workflows/awsfulltest_somatic.yml new file mode 100644 index 0000000000..367dee4870 --- /dev/null +++ b/.github/workflows/awsfulltest_somatic.yml @@ -0,0 +1,28 @@ +name: nf-core AWS full size tests somatic +# This workflow is triggered on published releases. +# It can be additionally triggered manually with GitHub actions workflow dispatch button. +# It runs the -profile 'test_full' on AWS batch + +on: + release: + types: [published] + workflow_dispatch: +jobs: + run-tower-somatic: + name: Run AWS full tests + if: github.repository == 'nf-core/sarek' + runs-on: ubuntu-latest + steps: + # Launch workflow using Tower CLI tool action + - name: Launch workflow via tower + uses: nf-core/tower-action@v3 + with: + workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} + compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/somatic_test + parameters: | + { + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/somatic_test" + } + profiles: test_full_somatic,aws_tower diff --git a/CHANGELOG.md b/CHANGELOG.md index ce32caf287..49943ad938 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -43,6 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#632](https://github.com/nf-core/sarek/pull/632) - Added params `--snpeff_version` to allow more configuration on the snpeff container definition - [#632](https://github.com/nf-core/sarek/pull/632) - Added params `--vep_include_fasta` to use the fasta file for annotation - [#639](https://github.com/nf-core/sarek/pull/639) - Adding genes-txt-file and summary-html-file to the published output from snpEff. +- [#652](https://github.com/nf-core/sarek/pull/652) - Added full size somatic test profile. ### Changed diff --git a/conf/test_full_somatic.config b/conf/test_full_somatic.config new file mode 100644 index 0000000000..2085078eed --- /dev/null +++ b/conf/test_full_somatic.config @@ -0,0 +1,27 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running full-size tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a full size pipeline test. + + Use as follows: + nextflow run nf-core/sarek -profile test_full_somatic, --outdir + +---------------------------------------------------------------------------------------- +*/ + +params { + config_profile_name = 'Full test profile for somatic VC' + config_profile_description = 'Full test dataset to check somatic VC pipeline function' + + // Input data for full size test + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test.csv' + + // Other params + tools = 'strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep' + genome = 'GATK.GRCh38' + schema_ignore_params = 'genomes' + wes = true + intervals = 's3://nf-core-awsmegatests/sarek/input/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed' + split_fastq = 20000000 +} diff --git a/nextflow.config b/nextflow.config index 7fecb8b14e..ccd16b18e9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -183,6 +183,7 @@ profiles { } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } + test_full_somatic { includeConfig 'conf/test_full_somatic.config' } } // Load igenomes.config if required