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Adding required R packages and SQANTI3/5.1.2 to Dockerfile #96

Adding required R packages and SQANTI3/5.1.2 to Dockerfile

Adding required R packages and SQANTI3/5.1.2 to Dockerfile #96

Workflow file for this run

name: tests
on:
workflow_dispatch:
push:
branches:
- master
- main
pull_request:
branches_ignore: []
jobs:
Dry_Run_and_Lint:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: docker://snakemake/snakemake:v5.24.2
- name: Dry Run with test data
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/bin/bash -c "cd /opt2 && /opt2/modr run --input \
/opt2/.tests/WT_S1_0.fastq.gz /opt2/.tests/WT_S1_1.fastq.gz \
/opt2/.tests/WT_S2_0.fastq.gz /opt2/.tests/WT_S2_1.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
/opt2/.tests/WT_S3_3.fastq.gz /opt2/.tests/WT_S3_4.fastq.gz \
/opt2/.tests/WT_S4.fastq.gz /opt2/.tests/WT_S5.fastq.gz \
--output /opt2/output --genome hg38_41 --groups /opt2/.tests/groups.tsv \
--mode local --dry-run"
- name: View the pipeline config file
run: |
echo "Generated config file for pipeline...." && cat $PWD/output/config.json
- name: Lint Workflow
continue-on-error: true
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \
echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'