Skip to content
tests

trim, bwa, and deduplication rules updated to work with single-end data #111

Sign in to view logs

trim, bwa, and deduplication rules updated to work with single-end data

trim, bwa, and deduplication rules updated to work with single-end data #111

Workflow file for this run

.github/workflows/main.yaml at eae51b2
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 cell-free ChIP-seq pipeline, all options
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.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the cfChIP pipeline config file
run: |
echo "Generated config file for cfChIP pipeline...." && cat $PWD/output/config.json
- name: Dry Run ChIP-seq pipeline, all options
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.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the ChIP pipeline config file
run: |
echo "Generated config file for ChIP pipeline...." && cat $PWD/output/config.json
- name: Dry Run ATAC-seq pipeline, all options
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 \
/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.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the ATAC pipeline config file
run: |
echo "Generated config file for ATAC pipeline...." && 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.'