Refactor codebase #174
Workflow file for this run
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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:v5.24.2 | |
| - name: Dry Run paired-end cell-free ChIP-seq pipeline, all options (with replicates, with inputs) | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/chrom-seek run --assay cfChIP --genome hg19 --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 \ | |
| /opt2/.tests/Input_S1.R1.fastq.gz /opt2/.tests/Input_S1.R2.fastq.gz \ | |
| /opt2/.tests/Input_S2_R1.fastq.gz /opt2/.tests/Input_S2_R2.fastq.gz \ | |
| /opt2/.tests/Input_S3_1.fastq.gz /opt2/.tests/Input_S3_2.fastq.gz \ | |
| /opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \ | |
| --output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_with_inputs.tsv \ | |
| --contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run | |
| - name: View the paired-end cfChIP pipeline config file (with replicates, with inputs) | |
| run: | | |
| echo "Generated config file for cfChIP pipeline (with replicates, with inputs)...." && cat $PWD/output/config.json | |
| - name: Dry Run paired-end cell-free ChIP-seq pipeline, all options (without replicates, with inputs) | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/chrom-seek run --assay cfChIP --genome hg19 --input \ | |
| /opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \ | |
| /opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \ | |
| /opt2/.tests/Input_S1.R1.fastq.gz /opt2/.tests/Input_S1.R2.fastq.gz \ | |
| /opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \ | |
| --output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_with_inputs.tsv \ | |
| --contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run | |
| - name: View the paired-end cfChIP pipeline config file (without replicates, with inputs) | |
| run: | | |
| echo "Generated config file for cfChIP pipeline (without replicates, with inputs)...." && cat $PWD/output/config.json | |
| - name: Dry Run paired-end ChIP-seq pipeline, all options (with replicates, with inputs) | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/chrom-seek run --assay ChIP --genome hg19 --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 \ | |
| /opt2/.tests/Input_S1.R1.fastq.gz /opt2/.tests/Input_S1.R2.fastq.gz \ | |
| /opt2/.tests/Input_S2_R1.fastq.gz /opt2/.tests/Input_S2_R2.fastq.gz \ | |
| /opt2/.tests/Input_S3_1.fastq.gz /opt2/.tests/Input_S3_2.fastq.gz \ | |
| /opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \ | |
| --output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_with_inputs.tsv \ | |
| --contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run | |
| - name: View the paired-end ChIP pipeline config file (with replicates, with inputs) | |
| run: | | |
| echo "Generated config file for ChIP pipeline (with replicates, with inputs)...." && cat $PWD/output/config.json | |
| - name: Dry Run paired-end ChIP-seq pipeline, all options (with replicates, without inputs) | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/chrom-seek run --assay ChIP --genome hg19 --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 --peakcall /opt2/.tests/peakcall_with_replicates_no_inputs.tsv \ | |
| --contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run | |
| - name: View the paired-end ChIP pipeline config file (with replicates, without inputs) | |
| run: | | |
| echo "Generated config file for ChIP pipeline (with replicates, without inputs)...." && cat $PWD/output/config.json | |
| - name: Dry Run paired-end ChIP-seq pipeline, all options (without replicates, with inputs) | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/chrom-seek run --assay ChIP --genome hg19 --input \ | |
| /opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \ | |
| /opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \ | |
| /opt2/.tests/Input_S1.R1.fastq.gz /opt2/.tests/Input_S1.R2.fastq.gz \ | |
| /opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \ | |
| --output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_with_inputs.tsv \ | |
| --contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run | |
| - name: View the paired-end ChIP pipeline config file (without replicates, with inputs) | |
| run: | | |
| echo "Generated config file for ChIP pipeline (without replicates, with inputs)...." && cat $PWD/output/config.json | |
| - name: Dry Run paired-end ChIP-seq pipeline, all options (without replicates, without inputs) | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/chrom-seek run --assay ChIP --genome hg19 --input \ | |
| /opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \ | |
| /opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \ | |
| --output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_no_inputs.tsv \ | |
| --contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run | |
| - name: View the paired-end ChIP pipeline config file (without replicates, without inputs) | |
| run: | | |
| echo "Generated config file for ChIP pipeline (without replicates, without inputs)...." && cat $PWD/output/config.json | |
| - name: Dry Run single-end ChIP-seq pipeline, all options (with replicates, with inputs) | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/chrom-seek run --assay ChIP --genome hg19 --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 \ | |
| /opt2/.tests/Input_S1.R1.fastq.gz \ | |
| /opt2/.tests/Input_S2_R1.fastq.gz \ | |
| /opt2/.tests/Input_S3_1.fastq.gz \ | |
| /opt2/.tests/Input_S4_R1.001.fastq.gz \ | |
| --output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_with_inputs.tsv \ | |
| --contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run | |
| - name: View the single-end ChIP pipeline config file (with replicates, with inputs) | |
| run: | | |
| echo "Generated config file for ChIP pipeline (with replicates, with inputs)...." && cat $PWD/output/config.json | |
| - name: Dry Run single-end ChIP-seq pipeline, all options (with replicates, without inputs) | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/chrom-seek run --assay ChIP --genome hg19 --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 --peakcall /opt2/.tests/peakcall_with_replicates_no_inputs.tsv \ | |
| --contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run | |
| - name: View the single-end ChIP pipeline config file (with replicates, without inputs) | |
| run: | | |
| echo "Generated config file for ChIP pipeline (with replicates, without inputs)...." && cat $PWD/output/config.json | |
| - name: Dry Run single-end ChIP-seq pipeline, all options (without replicates, with inputs) | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/chrom-seek run --assay ChIP --genome hg19 --input \ | |
| /opt2/.tests/WT_S1.R1.fastq.gz \ | |
| /opt2/.tests/WT_S4_R1.001.fastq.gz \ | |
| /opt2/.tests/Input_S1.R1.fastq.gz \ | |
| /opt2/.tests/Input_S4_R1.001.fastq.gz \ | |
| --output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_with_inputs.tsv \ | |
| --contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run | |
| - name: View the single-end ChIP pipeline config file (without replicates, with inputs) | |
| run: | | |
| echo "Generated config file for ChIP pipeline (without replicates, with inputs)...." && cat $PWD/output/config.json | |
| - name: Dry Run single-end ChIP-seq pipeline, all options (without replicates, without inputs) | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/chrom-seek run --assay ChIP --genome hg19 --input \ | |
| /opt2/.tests/WT_S1.R1.fastq.gz \ | |
| /opt2/.tests/WT_S4_R1.001.fastq.gz \ | |
| --output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_no_inputs.tsv \ | |
| --contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run | |
| - name: View the single-end ChIP pipeline config file (without replicates, without inputs) | |
| run: | | |
| echo "Generated config file for ChIP pipeline (without replicates, without inputs)...." && cat $PWD/output/config.json | |
| - name: Dry Run paired-end ATAC-seq pipeline, all options (with replicates, without inputs) | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/chrom-seek run --assay ATAC --genome hg19 --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 --peakcall /opt2/.tests/peakcall_with_replicates_no_inputs.tsv \ | |
| --contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run | |
| - name: View the paired-end ATAC pipeline config file (with replicates, without inputs) | |
| run: | | |
| echo "Generated config file for ATAC pipeline (with replicates, without inputs)...." && cat $PWD/output/config.json | |
| - name: Dry Run paired-end ATAC-seq pipeline, all options (without replicates, without inputs) | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/chrom-seek run --assay ATAC --genome hg19 --input \ | |
| /opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \ | |
| /opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \ | |
| --output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_no_inputs.tsv \ | |
| --contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run | |
| - name: View the paired-end ATAC pipeline config file (without replicates, without inputs) | |
| run: | | |
| echo "Generated config file for ATAC pipeline (without replicates, without inputs)...." && 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.' |