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new sra testing workflow
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ktmeaton committed Jun 17, 2020
1 parent 8f7c6d2 commit 673035d
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2 changes: 1 addition & 1 deletion .github/workflows/pipeline.yaml
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Expand Up @@ -68,5 +68,5 @@ jobs:
- name: artifact trace
uses: actions/upload-artifact@v2
with:
name: phylogeny
name: trace
path: test/trace/
63 changes: 63 additions & 0 deletions .github/workflows/sra.yaml
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@@ -0,0 +1,63 @@
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'

# Triggered on PR for all branches, pipeline
pull_request:
branches:
- '*'
# Also on a published release
release:
types: [published]

jobs:

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

#- 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

- 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/

- name: artifact trace
uses: actions/upload-artifact@v2
with:
name: trace
path: test/trace/
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -14,3 +14,4 @@ nextstrain/*.txt
nextstrain/test150/*
morelli2010/*
cui2013/*
EAGER_Ancient/*

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