• 📚 gpgr - Genomics Platform Group Reporting
  • Installation
  • Main modules
    • 🕸 LINX
    • 🔮 PURPLE
    • 🐍 umccrise
  • 🥳 Developers
  • 💻 CLI

📚 gpgr - Genomics Platform Group Reporting

Contains reports and functions used in the Genomics Platform Group at the University of Melbourne Centre for Cancer Research.

• Docs: https://umccr.github.io/gpgr/

Installation

remotes::install_github("umccr/gpgr")

• Or if used inside a conda environment:

conda install r-gpgr -c umccr -c conda-forge -c bioconda

Main modules

🕸 LINX

• Generate a HTML report with results from the LINX structural variant visualisation tool from the Hartwig Medical Foundation (https://github.com/hartwigmedical/hmftools/tree/master/linx). See the CLI section below for options.
• For useful functions for reading/processing LINX results, see the vignette at https://umccr.github.io/gpgr/articles/linx.html.

🔮 PURPLE

• Read and process output files from the PURPLE purity/copy number estimator tool from the Hartwig Medical Foundation (https://github.com/hartwigmedical/hmftools/tree/master/purple). See vignette at https://umccr.github.io/gpgr/articles/purple.html.

🐍 umccrise

• Generate a HTML report with results from the umccrise DRAGEN tumor/normal post-processing workflow from UMCCR - https://github.com/umccr/umccrise. See the CLI section below for options.

🥳 Developers

See https://umccr.github.io/gpgr/articles/devnotes.html for developer notes.

💻 CLI

A gpgr command line interface is available for convenience.

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

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

gpgr.R --version
gpgr.R 1.4.3

#-----------------------------------#
gpgr.R --help
usage: gpgr.R [-h] [-v] {linx,canrep} ...

UMCCR Genomics Platform Group Reporting

positional arguments:
  {linx,canrep}  sub-command help
    linx         UMCCR LINX Report.
    canrep       UMCCR Cancer Report.

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

#-----------------------------------#
#------- LINX Report -------#
gpgr.R linx --help
usage: gpgr.R linx [-h] --sample SAMPLE --plot PLOT --table TABLE [--out OUT]
                   [--quiet]

options:
  -h, --help       show this help message and exit
  --sample SAMPLE  Sample name.
  --plot PLOT      Path to LINX plot directory.
  --table TABLE    Path to LINX table directory.
  --out OUT        HTML output file name [def: linx_{sample}.html].
  --quiet          Suppress log printing during rendering.

#-----------------------------------#
#------- Cancer Report -------#
gpgr.R canrep --help
usage: gpgr.R canrep [-h] --af_global AF_GLOBAL --af_keygenes AF_KEYGENES
                     --batch_name BATCH_NAME --conda_list CONDA_LIST --img_dir
                     IMG_DIR --key_genes KEY_GENES --somatic_snv_summary
                     SOMATIC_SNV_SUMMARY --somatic_snv_vcf SOMATIC_SNV_VCF
                     --somatic_sv_tsv SOMATIC_SV_TSV --somatic_sv_vcf
                     SOMATIC_SV_VCF --purple_som_gene_cnv PURPLE_SOM_GENE_CNV
                     --purple_som_cnv PURPLE_SOM_CNV --purple_germ_cnv
                     PURPLE_GERM_CNV --purple_purity PURPLE_PURITY --purple_qc
                     PURPLE_QC --purple_som_snv_vcf PURPLE_SOM_SNV_VCF
                     --oncoviral_present_viruses ONCOVIRAL_PRESENT_VIRUSES
                     --oncoviral_breakpoints_tsv ONCOVIRAL_BREAKPOINTS_TSV
                     [--out_file OUT_FILE] [--quiet] --result_outdir
                     RESULT_OUTDIR --tumor_name TUMOR_NAME

options:
  -h, --help            show this help message and exit
  --af_global AF_GLOBAL
                        Path to `af_tumor.txt` file.
  --af_keygenes AF_KEYGENES
                        Path to `af_tumor_keygenes.txt` file.
  --batch_name BATCH_NAME
                        Name of batch sample.
  --conda_list CONDA_LIST
                        Path to `conda_pkg_list.txt` file.
  --img_dir IMG_DIR     Path to directory containing PURPLE plots.
  --key_genes KEY_GENES
                        Path to UMCCR cancer gene file.
  --somatic_snv_summary SOMATIC_SNV_SUMMARY
                        Path to `somatic_snv_summary.json`.
  --somatic_snv_vcf SOMATIC_SNV_VCF
                        Path to `somatic-PASS.vcf.gz` SNV VCF.
  --somatic_sv_tsv SOMATIC_SV_TSV
                        Path to `manta.tsv` TSV file.
  --somatic_sv_vcf SOMATIC_SV_VCF
                        Path to `manta.vcf.gz` VCF file.
  --purple_som_gene_cnv PURPLE_SOM_GENE_CNV
                        Path to `purple.cnv.gene.tsv`.
  --purple_som_cnv PURPLE_SOM_CNV
                        Path to `purple.cnv.somatic.tsv`.
  --purple_germ_cnv PURPLE_GERM_CNV
                        Path to `purple.cnv.germline.tsv`.
  --purple_purity PURPLE_PURITY
                        Path to `purple.purity.tsv`.
  --purple_qc PURPLE_QC
                        Path to `purple.qc`.
  --purple_som_snv_vcf PURPLE_SOM_SNV_VCF
                        Path to `purple.somatic.vcf.gz`.
  --oncoviral_present_viruses ONCOVIRAL_PRESENT_VIRUSES
                        Path to `oncoviruses/present_viruses.txt`.
  --oncoviral_breakpoints_tsv ONCOVIRAL_BREAKPOINTS_TSV
                        Path to `oncoviruses/oncoviral_breakpoints.tsv`.
  --out_file OUT_FILE   Path to output HTML file (needs '.html' suffix) [def:
                        {tumor_name}_cancer_report.html].
  --quiet               Suppress log printing during rendering.
  --result_outdir RESULT_OUTDIR
                        Path to directory to write tidy JSON/TSV results.
  --tumor_name TUMOR_NAME
                        Name of tumor sample.

#-----------------------------------#