fixed path to primer bed file #284
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name: DryRun | |
on: [push] | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v1 | |
- name: Help_test | |
run: curl -s https://get.nextflow.io | bash && ./nextflow run poreCov.nf --help | |
- name: fasta dry run | |
run: | | |
touch genome.fasta | |
./nextflow run poreCov.nf --fasta genome.fasta -stub -profile stub --cores 2 --max_cores 2 | |
- name: fastq dry run | |
run: | | |
touch reads.fastq | |
./nextflow run poreCov.nf --fastq reads.fastq -stub -profile stub --cores 2 --max_cores 2 | |
- name: fastq_pass dry run | |
run: | | |
mkdir fastq_pass | |
./nextflow run poreCov.nf --fastq_pass fastq_pass/ -stub -profile stub --cores 2 --max_cores 2 | |
- name: fast5 dry run | |
run: | | |
mkdir fast5 | |
./nextflow run poreCov.nf --fast5 fast5/ -stub -profile stub --cores 2 --max_cores 2 | |
- name: fast5 dry run nanopolish | |
run: | | |
mkdir fast5_2 | |
./nextflow run poreCov.nf --fast5 fast5_2/ --nanopolish -stub -profile stub --cores 2 --max_cores 2 | |
- name: fastq samples dry run | |
run: | | |
touch barcode01.fastq.gz | |
printf "_id,Status\nsample,BC01\n" > sample.csv | |
./nextflow run poreCov.nf --fastq barcode01.fastq.gz --samples sample.csv -stub -profile stub --cores 2 --max_cores 2 |