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added stub profiles for freyja and lcs screen-read processes #272

added stub profiles for freyja and lcs screen-read processes

added stub profiles for freyja and lcs screen-read processes #272

Workflow file for this run

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