Seperate ends #253
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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.' |