fix: mm10 kraken2 location #57
Workflow file for this run
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| name: tests | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| - unified | |
| pull_request: | |
| branches-ignore: [] | |
| jobs: | |
| Dry_Run_and_Lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: docker://snakemake/snakemake:v6.8.2 | |
| - name: Tumor-normal FastQ Dry Run | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \ | |
| /opt2/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \ | |
| /opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \ | |
| /opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.R2.fastq.gz \ | |
| --output /opt2/output_tn_fqs --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \ | |
| /opt2/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \ | |
| /opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \ | |
| /opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.R2.fastq.gz \ | |
| --output /opt2/output_tn_fqs --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun | |
| - name: Tumor-only FastQ Dry Run | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \ | |
| /opt2/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \ | |
| /opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \ | |
| /opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.R2.fastq.gz \ | |
| --output /opt2/output_tonly_fqs --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --genome hg38 --mode local --ffpe --runmode init | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \ | |
| /opt2/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \ | |
| /opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \ | |
| /opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.R2.fastq.gz \ | |
| --output /opt2/output_tonly_fqs --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --genome hg38 --mode local --ffpe --runmode dryrun | |
| - name: Tumor-normal BAM Dry Run | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \ | |
| /opt2/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.recal.bam \ | |
| /opt2/.tests/Sample11_ACI_158_S38.recal.bam \ | |
| /opt2/.tests/Sample4_CRL1622_S31.recal.bam \ | |
| --output /opt2/output_tn_bams --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \ | |
| /opt2/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.recal.bam \ | |
| /opt2/.tests/Sample11_ACI_158_S38.recal.bam \ | |
| /opt2/.tests/Sample4_CRL1622_S31.recal.bam \ | |
| --output /opt2/output_tn_bams --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun | |
| - name: Tumor-only BAM Dry Run | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \ | |
| /opt2/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.recal.bam \ | |
| /opt2/.tests/Sample11_ACI_158_S38.recal.bam \ | |
| /opt2/.tests/Sample4_CRL1622_S31.recal.bam \ | |
| --output /opt2/output_tonly_bams --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --genome hg38 --mode local --ffpe --runmode init | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \ | |
| /opt2/xavier run --input \ | |
| /opt2/.tests/Sample10_ARK1_S37.recal.bam \ | |
| /opt2/.tests/Sample11_ACI_158_S38.recal.bam \ | |
| /opt2/.tests/Sample4_CRL1622_S31.recal.bam \ | |
| --output /opt2/output_tonly_bams --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \ | |
| --genome hg38 --mode local --ffpe --runmode dryrun | |
| - 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_tn_fqs || \ | |
| echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.' |