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.drone.yml
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.drone.yml
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pipeline:
quant:
image: combinelab/continuous_analysis_rnaseq:latest
volumes:
- /continuous_analysis_data/rna:/rna
commands:
- ls /rna
- mkdir -p salmon_output
- salmon index -i mm10 -t /rna/refMrna.fa.gz
- salmon quant -i mm10 -o salmon_output/SRR1654626 --numBootstraps 10 -l A -1 /rna/SRR1654626_1.fastq.gz -2 /rna/SRR1654626_2.fastq.gz -p 28
- salmon quant -i mm10 -o salmon_output/SRR1654628 --numBootstraps 10 -l A -1 /rna/SRR1654628_1.fastq.gz -2 /rna/SRR1654628_2.fastq.gz -p 28
- salmon quant -i mm10 -o salmon_output/SRR1654633 --numBootstraps 10 -l A -1 /rna/SRR1654633_1.fastq.gz -2 /rna/SRR1654633_2.fastq.gz -p 28
- salmon quant -i mm10 -o salmon_output/SRR1654636 --numBootstraps 10 -l A -1 /rna/SRR1654636_1.fastq.gz -2 /rna/SRR1654636_2.fastq.gz -p 28
- salmon quant -i mm10 -o salmon_output/SRR1654637 --numBootstraps 10 -l A -1 /rna/SRR1654637_1.fastq.gz -2 /rna/SRR1654637_2.fastq.gz -p 28
- salmon quant -i mm10 -o salmon_output/SRR1654639 --numBootstraps 10 -l A -1 /rna/SRR1654639_1.fastq.gz -2 /rna/SRR1654639_2.fastq.gz -p 28
- salmon quant -i mm10 -o salmon_output/SRR1654641 --numBootstraps 10 -l A -1 /rna/SRR1654641_1.fastq.gz -2 /rna/SRR1654641_2.fastq.gz -p 28
- salmon quant -i mm10 -o salmon_output/SRR1654643 --numBootstraps 10 -l A -1 /rna/SRR1654643_1.fastq.gz -2 /rna/SRR1654643_2.fastq.gz -p 28
- mkdir -p results
- Rscript r_script.r
- git config user.email "rob.patro@cs.stonybrook.edu"
- git config user.name "Rob Patro"
- git config --global push.default simple
- git remote set-url origin git@github.com:COMBINE-lab/continuous_analysis_rnaseq.git
- git checkout master
- git add salmon_output
- git add results
- git commit -a -m "Drone Build [skip ci] [ci skip]"
git_push:
image: plugins/git-push
branch: master
remote: git@github.com:COMBINE-lab/continuous_analysis_rnaseq.git
force: true
branches: salmon-pipeline