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name: SRA | ||
#This is a workflow for speciality pipeline feature, SRA Download | ||
on: | ||
# Triggered on Push for any branch | ||
push: | ||
branches: | ||
- '*' | ||
# On change to workflow, pipeline | ||
paths: | ||
- '.github/workflows/sra.yaml' | ||
- 'pipeline.nf' | ||
- 'phylo-env.yaml' | ||
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# Triggered on PR for all branches, pipeline | ||
pull_request: | ||
branches: | ||
- '*' | ||
# Also on a published release | ||
release: | ||
types: [published] | ||
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jobs: | ||
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pipeline: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v2 | ||
- uses: goanpeca/setup-miniconda@v1 | ||
with: | ||
activate-environment: phylo-env | ||
environment-file: phylo-env.yaml | ||
auto-activate-base: false | ||
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#- name: pull eager | ||
# shell: bash -l {0} | ||
# run: | | ||
# nextflow pull nf-core/eager -r b2b411b | ||
# cp ~/.nextflow/assets/nf-core/eager/environment.yml eager-env.yaml | ||
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- name: pipeline | ||
shell: bash -l {0} | ||
run: | | ||
nextflow run pipeline.nf \ | ||
--sqlite results/ncbimeta_db/update/latest/output/database/yersinia_pestis_db.sqlite \ | ||
--outdir test \ | ||
--sqlite_select_command_sra "\"SELECT BioSampleAccession,SRARunAccession,SRALibraryLayout,SRAFileURL FROM Master WHERE (SRARunAccession = 'SRR1048902' OR SRARunAccession = 'SRR1048905')\"" \ | ||
--max_datasets_sra 10 \ | ||
--skip_assembly_download \ | ||
--skip_eager \ | ||
--skip_reference_download \ | ||
-resume | ||
- name: artifact SQLite import | ||
uses: actions/upload-artifact@v2 | ||
with: | ||
name: sqlite-import | ||
path: test/sqlite_import/ | ||
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- name: artifact trace | ||
uses: actions/upload-artifact@v2 | ||
with: | ||
name: trace | ||
path: test/trace/ |
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@@ -14,3 +14,4 @@ nextstrain/*.txt | |
nextstrain/test150/* | ||
morelli2010/* | ||
cui2013/* | ||
EAGER_Ancient/* |