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Get basename of FILENAME awk #82

Get basename of FILENAME awk

Get basename of FILENAME awk #82

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 Paired-end
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/metavirs run --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
--output /opt2/output --mode local --aggregate --dry-run
- name: Dry Run with Single-end
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/metavirs run --input \
/opt2/.tests/WT_S1.R1.fastq.gz \
/opt2/.tests/WT_S2_R1.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz \
--output /opt2/output --mode local --aggregate --dry-run
- name: Dry Run with Mixed
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/metavirs run --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S2_R1.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz \
--output /opt2/output --mode local --aggregate --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.'