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Adding all possible dry-run combinations for cfChIP, ChIP, and ATAC.
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‎.github/workflows/main.yaml‎

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@@ -15,7 +15,7 @@ jobs:
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steps:
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- uses: actions/checkout@v2
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- uses: docker://snakemake/snakemake:v5.24.2
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- name: Dry Run cell-free ChIP-seq pipeline, all options
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- name: Dry Run paired-end cell-free ChIP-seq pipeline, all options (with replicates, with inputs)
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run: |
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docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
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/opt2/chrom-seek run --assay cfChIP --genome hg19 --input \
@@ -27,12 +27,25 @@ jobs:
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/opt2/.tests/Input_S2_R1.fastq.gz /opt2/.tests/Input_S2_R2.fastq.gz \
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/opt2/.tests/Input_S3_1.fastq.gz /opt2/.tests/Input_S3_2.fastq.gz \
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/opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \
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--output /opt2/output --peakcall /opt2/.tests/peakcall.tsv \
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--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_with_inputs.tsv \
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--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
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- name: View the cfChIP pipeline config file
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- name: View the paired-end cfChIP pipeline config file (with replicates, with inputs)
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run: |
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echo "Generated config file for cfChIP pipeline...." && cat $PWD/output/config.json
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- name: Dry Run ChIP-seq pipeline, all options
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echo "Generated config file for cfChIP pipeline (with replicates, with inputs)...." && cat $PWD/output/config.json
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- name: Dry Run paired-end cell-free ChIP-seq pipeline, all options (without replicates, with inputs)
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run: |
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docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
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/opt2/chrom-seek run --assay cfChIP --genome hg19 --input \
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/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
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/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
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/opt2/.tests/Input_S1.R1.fastq.gz /opt2/.tests/Input_S1.R2.fastq.gz \
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/opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \
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--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_with_inputs.tsv \
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--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
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- name: View the paired-end cfChIP pipeline config file (without replicates, with inputs)
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run: |
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echo "Generated config file for cfChIP pipeline (without replicates, with inputs)...." && cat $PWD/output/config.json
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- name: Dry Run paired-end ChIP-seq pipeline, all options (with replicates, with inputs)
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run: |
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docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
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/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
@@ -44,28 +57,126 @@ jobs:
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/opt2/.tests/Input_S2_R1.fastq.gz /opt2/.tests/Input_S2_R2.fastq.gz \
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/opt2/.tests/Input_S3_1.fastq.gz /opt2/.tests/Input_S3_2.fastq.gz \
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/opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \
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--output /opt2/output --peakcall /opt2/.tests/peakcall.tsv \
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--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_with_inputs.tsv \
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--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
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- name: View the ChIP pipeline config file
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- name: View the paired-end ChIP pipeline config file (with replicates, with inputs)
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run: |
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echo "Generated config file for ChIP pipeline...." && cat $PWD/output/config.json
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- name: Dry Run ATAC-seq pipeline, all options
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echo "Generated config file for ChIP pipeline (with replicates, with inputs)...." && cat $PWD/output/config.json
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- name: Dry Run paired-end ChIP-seq pipeline, all options (with replicates, without inputs)
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run: |
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docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
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/opt2/chrom-seek run --assay ATAC --genome hg19 --input \
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/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
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/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
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/opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \
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/opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
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/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
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--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_no_inputs.tsv \
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--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
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- name: View the paired-end ChIP pipeline config file (with replicates, without inputs)
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run: |
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echo "Generated config file for ChIP pipeline (with replicates, without inputs)...." && cat $PWD/output/config.json
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- name: Dry Run paired-end ChIP-seq pipeline, all options (without replicates, with inputs)
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run: |
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docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
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/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
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/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
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/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
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/opt2/.tests/Input_S1.R1.fastq.gz /opt2/.tests/Input_S1.R2.fastq.gz \
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/opt2/.tests/Input_S2_R1.fastq.gz /opt2/.tests/Input_S2_R2.fastq.gz \
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/opt2/.tests/Input_S3_1.fastq.gz /opt2/.tests/Input_S3_2.fastq.gz \
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/opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \
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--output /opt2/output --peakcall /opt2/.tests/peakcall.tsv \
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--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_with_inputs.tsv \
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--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
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- name: View the paired-end ChIP pipeline config file (without replicates, with inputs)
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run: |
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echo "Generated config file for ChIP pipeline (without replicates, with inputs)...." && cat $PWD/output/config.json
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- name: Dry Run paired-end ChIP-seq pipeline, all options (without replicates, without inputs)
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run: |
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docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
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/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
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/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
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/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
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--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_no_inputs.tsv \
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--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
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- name: View the paired-end ChIP pipeline config file (without replicates, without inputs)
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run: |
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echo "Generated config file for ChIP pipeline (without replicates, without inputs)...." && cat $PWD/output/config.json
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- name: Dry Run single-end ChIP-seq pipeline, all options (with replicates, with inputs)
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run: |
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docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
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/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
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/opt2/.tests/WT_S1.R1.fastq.gz \
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/opt2/.tests/WT_S2_R1.fastq.gz \
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/opt2/.tests/WT_S3_1.fastq.gz \
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/opt2/.tests/WT_S4_R1.001.fastq.gz \
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/opt2/.tests/Input_S1.R1.fastq.gz \
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/opt2/.tests/Input_S2_R1.fastq.gz \
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/opt2/.tests/Input_S3_1.fastq.gz \
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/opt2/.tests/Input_S4_R1.001.fastq.gz \
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--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_with_inputs.tsv \
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--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
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- name: View the single-end ChIP pipeline config file (with replicates, with inputs)
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run: |
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echo "Generated config file for ChIP pipeline (with replicates, with inputs)...." && cat $PWD/output/config.json
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- name: Dry Run single-end ChIP-seq pipeline, all options (with replicates, without inputs)
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run: |
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docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
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/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
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/opt2/.tests/WT_S1.R1.fastq.gz \
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/opt2/.tests/WT_S2_R1.fastq.gz \
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/opt2/.tests/WT_S3_1.fastq.gz \
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/opt2/.tests/WT_S4_R1.001.fastq.gz \
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--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_no_inputs.tsv \
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--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
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- name: View the single-end ChIP pipeline config file (with replicates, without inputs)
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run: |
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echo "Generated config file for ChIP pipeline (with replicates, without inputs)...." && cat $PWD/output/config.json
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- name: Dry Run single-end ChIP-seq pipeline, all options (without replicates, with inputs)
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run: |
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docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
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/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
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/opt2/.tests/WT_S1.R1.fastq.gz \
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/opt2/.tests/WT_S4_R1.001.fastq.gz \
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/opt2/.tests/Input_S1.R1.fastq.gz \
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/opt2/.tests/Input_S4_R1.001.fastq.gz \
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--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_with_inputs.tsv \
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--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
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- name: View the single-end ChIP pipeline config file (without replicates, with inputs)
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run: |
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echo "Generated config file for ChIP pipeline (without replicates, with inputs)...." && cat $PWD/output/config.json
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- name: Dry Run single-end ChIP-seq pipeline, all options (without replicates, without inputs)
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run: |
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docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
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/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
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/opt2/.tests/WT_S1.R1.fastq.gz \
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/opt2/.tests/WT_S4_R1.001.fastq.gz \
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--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_no_inputs.tsv \
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--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
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- name: View the single-end ChIP pipeline config file (without replicates, without inputs)
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run: |
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echo "Generated config file for ChIP pipeline (without replicates, without inputs)...." && cat $PWD/output/config.json
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- name: Dry Run paired-end ATAC-seq pipeline, all options (with replicates, without inputs)
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run: |
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docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
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/opt2/chrom-seek run --assay ATAC --genome hg19 --input \
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/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
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/opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \
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/opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
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/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
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--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_no_inputs.tsv \
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--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
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- name: View the paired-end ATAC pipeline config file (with replicates, without inputs)
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run: |
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echo "Generated config file for ATAC pipeline (with replicates, without inputs)...." && cat $PWD/output/config.json
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- name: Dry Run paired-end ATAC-seq pipeline, all options (without replicates, without inputs)
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run: |
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docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
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/opt2/chrom-seek run --assay ATAC --genome hg19 --input \
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/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
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/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
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--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_no_inputs.tsv \
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--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
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- name: View the ATAC pipeline config file
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- name: View the paired-end ATAC pipeline config file (without replicates, without inputs)
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run: |
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echo "Generated config file for ATAC pipeline...." && cat $PWD/output/config.json
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echo "Generated config file for ATAC pipeline (without replicates, without inputs)...." && cat $PWD/output/config.json
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- name: Lint Workflow
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continue-on-error: true
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run: |

‎.tests/peakcall_no_replicates_no_inputs.tsv‎

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ChIP Group
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WT_S1 G1
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WT_S4 G2

‎.tests/peakcall_no_replicates_with_inputs.tsv‎

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ChIP Input Group
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WT_S1 Input_S1 G1
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WT_S4 Input_S4 G2

‎.tests/peakcall_with_replicates_no_inputs.tsv‎

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ChIP Input
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WT_S1 Input_S1
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WT_S2 Input_S2
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WT_S3 Input_S3
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WT_S4 Input_S4

‎.tests/peakcall_with_replicates_with_inputs.tsv‎

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peakcall.tsv

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