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CRomwell Output Organizer

Project description

Cromweller Output Organizer (COO)

COO is a Python package for organizing outputs from Cromwell.


COO takes in metadata.json which is generated from Cromwell and parses it to get information about all outputs. Then it makes a copy (or a soft link) of each output file as described in an output definition JSON file specified by --out-def-json.


  • Automatic file transfer between local/cloud storages: For example, the following command line works. You can define URIs instead of local path for any command line arguments. The following command line reads from remote metadata JSON file (gs://some/where/metadata.json) and output definition JSON file (s3://over/here/atac.out_def.json) and write organized outputs to gs://your/final/out/bucket.

     $ coo gs://some/where/metadata.json --out-def-json s3://over/here/atac.out_def.json --out-dir gs://your/final/out/bucket
  • Soft-linking (local storage only): COO defaults to make soft links instead of copying for local-to-local file transfer (local output file defined in a metadata JSON vs. local output directory specifed by --out-dir). In order to force copying instead of soft-linking regardless of a storage type then use --method copy. Local-to-cloud and cloud-to-local file transfer always uses copy method.

Output definition JSON file

An output definition JSON file must be provided for a corresponding WDL file.

For the following example of ENCODE ATAC-Seq pipeline, atac.bowtie2 is a task called in a scatter {} block iterating over biological replicates so that the type of an output variable atac.bowtie2.bam in a workflow level is Array[File]. Therefore, we need an index for the scatter {} iteration to have access to each file that bam points to. An inline expression like ${i} (0-based) allows access to such index. ${basename} refers to the basename of the original output file. BAM and flagstat log from atac.bowtie2 will be transferred to different locations align/repX/ and qc/repX/, respectively. atac.qc_report is a final task of a workflow gathering all QC logs so it's not called in a scatter {} block. There shouldn't be any scatter indices like i0, i1, j0 and j1.


  "atac.bowtie2": {
    "bam": {
      "path": "align/rep${i+1}/${basename}",
    "flagstat_qc": {
      "path": "qc/rep${i+1}/${basename}",
  "atac.qc_report": {
    "report": {
      "path": "qc/final_qc_report.html"
    "qc_json": {
      "path": "qc/final_qc.json"

More generally for subworkflows a definition JSON file looks like the following:

    "[OUT_VAR_NAME_IN_TASK]" : {
      "path": "[OUT_REL_PATH_DEF]"

    "[OUT_VAR_NAME_IN_TASK]" : {
      "path": "[OUT_REL_PATH_DEF]"

WARNING: Unfortunately, for an output variable [OUT_VAR_NAME_IN_TASK] in a task COO does not currently support Array[File] type. It only supports File type. task t1 { command { ... } output { Array[File] out_list # NOT SUPPORTED File out # SUPPORTED } }

{ "path" : "[OUT_REL_PATH_DEF]" } defines a final output destination. It's a file path RELATIVE to the output directory species as --out-dir. The following inline expressions are allowe for [OUT_REL_PATH_DEF]. You can use basic Python expressions inside ${}. For example, ${basename.split(".")[0]} should be helpful to get the prefix of a file like some_prefix.fastqs.gz.

Built-in variable Type Description
basename str Basename of file
dirname str Dirname of file
full_path str Full path of file
i int 0-based index for main scatter loop
j int 0-based index for nested scatter loop
k int 0-based index for double-nested scatter loop
shard_idx tuple(int) tuple of indices for each dim.: (i, j, k, ...)


We will add PIP installation later. Until then git clone it and manually add coo to your environment variable PATH in your BASH startup scripts (~/.bashrc). Make sure that you have python3 >=3.3 installed on your system.

$ git clone
$ echo "export PATH=\"\$PATH:$PWD/cromwell_output_organizer\"" >> ~/.bashrc

Inter-storage file transfer

In order to use auto-transfer between local/cloud storages, you need to configure for corresponding cloud CLI (gsutil or aws) for a target storage. Refer to here for details.

WARNING: COO does not ensure a fail-safe file transfer when it's interrupted by user or system. Also, there can be race conditions if multiple users try to access/copy files. This will be later addressed in the future release. Until then DO NOT interrupt COO until you see the following copying done message.


usage: coo [-h] --out-def-json OUT_DEF_JSON [--method {link,copy}]
           [--out-dir OUT_DIR] [--tmp-dir TMP_DIR] [--use-gsutil-over-aws-s3]
           [--http-user HTTP_USER] [--http-password HTTP_PASSWORD]

positional arguments:
  metadata_json         Path, URL or URI for metadata.json for a workflow
                        Example: /scratch/sample1/metadata.json,

optional arguments:
  -h, --help            show this help message and exit
  --out-def-json OUT_DEF_JSON
                        Output definition JSON file for a WDL file
                        corresponding to the specified metadata.json file
  --method {link,copy}  Method to localize files on output directory/bucket.
                        "link" means a soft-linking and it's for local
                        directory only. Original output files will be kept in
                        Cromwell's output directory. "copy" makes a copy of
                        Cromwell's original outputs
  --out-dir OUT_DIR     Output directory/bucket
  --tmp-dir TMP_DIR     Temporary local directory
                        Use gsutil instead of aws s3 CLI even for S3 buckets.
  --http-user HTTP_USER
                        Username to download data from private URLs
  --http-password HTTP_PASSWORD
                        Password to download data from private URLs


  • python >= 3.3, pip3, wget and curl


     $ sudo apt-get install python3 python3-pip wget curl


     $ sudo yum install python3 epel-release wget curl
  • gsutil: Run the followings to configure for gsutil:

     $ gcloud auth login --no-launch-browser
     $ gcloud auth application-default --no-launch-browser
  • AWS CLI: Run the followings to configure for AWS CLI:

     $ aws configure

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