Merge remote-tracking branch 'upstream/dev' into file_structure

nf-core · Jul 18, 2022 · ef7f9cb · ef7f9cb
2 parents 3b576c1 + 9afe650
commit ef7f9cb
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Showing 5 changed files with 59 additions and 2 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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,<docker/singularity> --outdir <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
@@ -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