Updating rule all with new targets of GATK best-practices sub workflo… #231
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| 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:v7.25.3 | |
| - name: Dry Run WGS pipeline with test data, all options | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.25.3 \ | |
| /opt2/genome-seek 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 --pairs /opt2/.tests/pairs.tsv \ | |
| --call-hla --call-sv --call-cnv --call-somatic --open-cravat \ | |
| --oc-annotators encode_tfbs ccre_screen vista_enhancer gnomad3 thousandgenomes cadd \ | |
| --pon /opt2/.tests/1000g_pon.hg38.vcf.gz --dry-run | |
| - name: Dry Run WES pipeline with test data, all options | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.25.3 \ | |
| /opt2/genome-seek 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 --pairs /opt2/.tests/pairs.tsv \ | |
| --call-hla --call-sv --call-cnv --call-somatic --open-cravat \ | |
| --oc-annotators encode_tfbs ccre_screen vista_enhancer gnomad3 thousandgenomes cadd \ | |
| --pon /opt2/.tests/1000g_pon.hg38.vcf.gz \ | |
| --wes-mode --wes-bed /opt2/.tests/wes_regions.bed --dry-run | |
| - name: Dry Run WGS pipeline with test data, skip QC | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.25.3 \ | |
| /opt2/genome-seek 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 --skip-qc --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:v7.25.3 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.' |