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Use gzip instead of pigz for kraken2 output compression #158

Use gzip instead of pigz for kraken2 output compression

Use gzip instead of pigz for kraken2 output compression #158

name: Validate syntax and DAG
on:
push:
branches:
- master
- develop
pull_request: [] # Do it on all PRs
jobs:
validate-syntax-and-dag:
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
docker_tag:
- 'stable'
container:
image: snakemake/snakemake:${{ matrix.docker_tag }}
name: Validate syntax and DAG
steps:
- name: Check out code
uses: actions/checkout@v3
- name: Create empty input files
run: |
ls
mkdir -pv input
touch input/test1_1.fq.gz input/test1_2.fq.gz
touch input/test2_1.fq.gz input/test2_2.fq.gz
- name: Create placeholder db files
run: |
ls
mkdir -pv tmpdir
mkdir -pv db/hg19
mkdir -pv db/metaphlan
touch db/hg19/taxo.k2d
touch db/metaphlan/test.1.bt2
- name: Modify config.yaml
run: |
ls
sed -i 's/assess_depth: False/assess_depth: True/' config/config.yaml
sed -i 's/sketch_compare: False/sketch_compare: True/' config/config.yaml
sed -i 's/kaiju: False/kaiju: True/' config/config.yaml
sed -i 's/kraken2: False/kraken2: True/' config/config.yaml
sed -i 's/metaphlan: False/metaphlan: True/' config/config.yaml
sed -i 's/humann: False/humann: True/' config/config.yaml
sed -i 's/strainphlan: False/strainphlan: True/' config/config.yaml
sed -i 's/groot: False/groot: True/' config/config.yaml
sed -i 's/amrplusplus: False/amrplusplus: True/' config/config.yaml
sed -i 's/assembly: False/assembly: True/' config/config.yaml
sed -i 's/binning: False/binning: True/' config/config.yaml
sed -i 's|db_path: \"\"|db_path: \"db/hg19\"|' config/config.yaml
sed -i 's|db: \"\"|db: \"db\"|' config/config.yaml
sed -i 's|bt2_db_dir: \"\"|bt2_db_dir: \"db/metaphlan\"|' config/config.yaml
sed -i 's|bt2_index: \"\"|bt2_index: \"test\"|' config/config.yaml
sed -i 's|_db: \"\"|_db: \"db\"|' config/config.yaml
sed -i 's| index: \"\"| index: \"db\"|' config/config.yaml
sed -i 's|kmer_distrib: \"\"|kmer_distrib: \"db\"|' config/config.yaml
sed -i 's|tmpdir: \"/scratch\"|tmpdir: \"tmpdir\"|' config/config.yaml
cat config/config.yaml
- name: Run Snakemake
run: |
ls
snakemake --dryrun