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Tutorial for general UNIX computers with docker

  1. Download cromwell.

    $ cd
$ wget https://github.com/broadinstitute/cromwell/releases/download/34/cromwell-34.jar
$ chmod +rx cromwell-34.jar

  2. Git clone this pipeline and move into it.

    $ cd
$ git clone https://github.com/ENCODE-DCC/atac-seq-pipeline
$ cd atac-seq-pipeline

  3. Download a SUBSAMPLED (1/400) paired-end sample of ENCSR356KRQ.

    $ wget https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/ENCSR356KRQ_fastq_subsampled.tar
$ tar xvf ENCSR356KRQ_fastq_subsampled.tar

  4. Download pre-built genome database for hg38.

    $ wget https://storage.googleapis.com/encode-pipeline-genome-data/test_genome_database_hg38_atac.tar
$ tar xvf test_genome_database_hg38_atac.tar

  5. Run a pipeline for the test sample.

    $ INPUT=examples/local/ENCSR356KRQ_subsampled.json
$ PIPELINE_METADATA=metadata.json
$ java -jar -Dconfig.file=backends/backend.conf cromwell-34.jar run atac.wdl -i ${INPUT} -o workflow_opts/docker.json -m ${PIPELINE_METADATA}

  6. It will take about an hour. You will be able to find all outputs on cromwell-executions/atac/[RANDOM_HASH_STRING]/. See output directory structure for details.

  7. See full specification for input JSON file.

  8. You can resume a failed pipeline from where it left off by using PIPELINE_METADATA(metadata.json) file. This file is created for each pipeline run. See here for details. Once you get a new input JSON file from the resumer, use it INPUT=resume.[FAILED_WORKFLOW_ID].json instead of INPUT=examples/local/ENCSR356KRQ_subsampled.json.