🔥 dracarys - UMCCR Workflow Tidying

🔥 dracarys - UMCCR Workflow Tidying

Docs: https://umccr.github.io/dracarys/

🏆 Aim

Given a directory with results from a DRAGEN/UMCCR workflow, {dracarys} will grab files of interest and transform them into ‘tidier’ structures for output into TSV/Parquet/RDS format for downstream ingestion into a database/data lake. See supported workflows, running examples, and CLI options in the sections below.

🍕 Installation

``` r remotes::install_github("umccr/dracarys@vX.X.X") # for vX.X.X Release/Tag ```

Conda

- Linux & MacOS (non-M1) ``` bash mamba create \ -n dracarys_env \ -c umccr -c bioconda -c conda-forge \ r-dracarys==X.X.X conda activate dracarys_env ``` - MacOS M1 ``` bash CONDA_SUBDIR=osx-64 \ mamba create \ -n dracarys_env \ -c umccr -c bioconda -c conda-forge \ r-dracarys==X.X.X conda activate dracarys_env ```

Docker

``` bash docker pull --platform linux/amd64 ghcr.io/umccr/dracarys:X.X.X ```

✨ Supported Workflows

{dracarys} supports most outputs from the following DRAGEN/UMCCR workflows:

Workflow	Description
bcl_convert	BCLConvert workflow
tso_ctdna_tumor_only	ctDNA TSO500 workflow
wgs_alignment_qc	DRAGEN DNA (alignment) workflow
wts_alignment_qc	DRAGEN RNA (alignment) workflow
wts_tumor_only	DRAGEN RNA workflow
wgs_tumor_normal	DRAGEN Tumor/Normal workflow
umccrise	umccrise workflow
rnasum	RNAsum workflow
sash	sash workflow
oncoanalyser	oncoanalyser workflow

See which output files from these workflows are supported in Supported Files.

🌀 CLI

A dracarys.R command line interface is available for convenience.

If you’re using the conda package, the dracarys.R command will already be available inside the activated conda environment.
If you’re not using the conda package, you need to export the dracarys/inst/cli/ directory to your PATH in order to use dracarys.R.

dracarys_cli=$(Rscript -e 'x = system.file("cli", package = "dracarys"); cat(x, "\n")' | xargs)
export PATH="${dracarys_cli}:${PATH}"

dracarys.R --version
dracarys.R 0.16.0

#-----------------------------------#
dracarys.R --help
usage: dracarys.R [-h] [-v] {tidy} ...

🐉 DRAGEN Output Post-Processing 🔥

positional arguments:
  {tidy}         sub-command help
    tidy         Tidy UMCCR Workflow Outputs

options:
  -h, --help     show this help message and exit
  -v, --version  show program's version number and exit

#-----------------------------------#
#------- Tidy ----------------------#
dracarys.R tidy --help
usage: dracarys.R tidy [-h] -i IN_DIR -o OUT_DIR -p PREFIX [-t TOKEN]
                       [-l LOCAL_DIR] [-f FORMAT] [-n] [-q]

options:
  -h, --help            show this help message and exit
  -i IN_DIR, --in_dir IN_DIR
                        ⛄️ Directory with untidy UMCCR workflow results. Can
                        be GDS, S3 or local.
  -o OUT_DIR, --out_dir OUT_DIR
                        🔥 Directory to output tidy results.
  -p PREFIX, --prefix PREFIX
                        🎻 Prefix string used for all results.
  -t TOKEN, --token TOKEN
                        🙈 ICA access token. Default: ICA_ACCESS_TOKEN env var.
  -l LOCAL_DIR, --local_dir LOCAL_DIR
                        📥 If input is a GDS/S3 directory, download the
                        recognisable files to this directory. Default:
                        '<out_dir>/dracarys_<gds|s3>_sync'.
  -f FORMAT, --format FORMAT
                        🎨 Format of output. Default: tsv.
  -n, --dryrun          🐫 Dry run - just show files to be tidied.
  -q, --quiet           😴 Shush all the logs.

🚕 Running

{dracarys} takes as input (--in_dir) a directory with results from one of the UMCCR workflows. It will recursively scan that directory for supported files, download those into a local directory (--gds_local_dir), and then it will parse, transform and write the tidied versions into the specified output directory (--out_dir). A prefix (--prefix) is prepended to each of the tidied files. The output file format (--format) can be tsv, parquet, or both. To get just a list of supported files within the specified input directory, use the -n (--dryrun) option.

``` r # help(umccr_tidy) in_dir <- "gds://path/to/subjectX_multiqc_data/" out_dir <- tempdir() prefix <- "subjectX" umccr_tidy(in_dir = in_dir, out_dir = out_dir, prefix = prefix) ```

Mac/Linux

From within an activated conda environment or a shell with the `dracarys.R` CLI available: ``` bash dracarys.R tidy \ -i gds://path/to/subjectX_multiqc_data/ \ -o local_output_dir \ -p subjectX_prefix ```