From 71627d550625c4c999d4b8d55f709451f7dc6bc6 Mon Sep 17 00:00:00 2001 From: skchronicles Date: Mon, 10 Jun 2024 13:09:09 -0400 Subject: [PATCH] Adding gatk-germline cli option --- README.md | 4 ++-- genome-seek | 26 ++++++++++++++++++++++---- 2 files changed, 24 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index cbd65a8..c51f174 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ Before getting started, we highly recommend reading through the [usage](https:// For more information about issues or troubleshooting a problem, please check out our [FAQ](https://openomics.github.io/genome-seek/faq/questions/) before [opening an issue on Github](https://github.com/OpenOmics/genome-seek/issues). ## Dependencies -**Requires:** `singularity>=3.5` `snakemake>=7.8` +**Requires:** `singularity>=3.5` `snakemake<=7.32.3` At the current moment, the pipeline only has two dependencies: snakemake and singularity/apptainer. With that being said, [snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) and ([singularity](https://singularity.lbl.gov/all-releases) or [apptainer](https://apptainer.org/docs/admin/main/installation.html)) must be installed on the target system. Snakemake orchestrates the execution of each step in the pipeline. The second dependency, i.e singularity/apptainer, handles downloading/distribution of the pipeline's software dependencies. To guarantee the highest level of reproducibility, each step of the pipeline relies on versioned images from [DockerHub](https://hub.docker.com/repositories/skchronicles). Snakemake uses singularity to pull these images onto the local filesystem prior to job execution, and as so, snakemake and singularity/apptainer will be the only two dependencies in the future. @@ -53,4 +53,4 @@ This site is a living document, created for and by members like you. genome-seek ## References **1.** Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459. -**2.** Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600. \ No newline at end of file +**2.** Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600. diff --git a/genome-seek b/genome-seek index d9980d4..4436f1a 100755 --- a/genome-seek +++ b/genome-seek @@ -5,7 +5,7 @@ ABOUT: This is the main entry for the pipeline. REQUIRES: - python>=3.6 - - snakemake (recommended>=6.0.0) + - snakemake (required<8.0.0) - singularity (recommended==latest) DISCLAIMER: PUBLIC DOMAIN NOTICE @@ -362,10 +362,10 @@ def parsed_arguments(name, description): {3}{4}Synopsis:{5} $ {2} run [--help] \\ [--mode {{slurm,uge,local}}] [--job-name JOB_NAME] [--batch-id BATCH_ID] \\ - [--call-cnv] [--call-sv] [--call-hla] [--call-somatic] [--open-cravat] \\ - [--skip-qc] [--oc-annotators OC_ANNOTATORS] [--oc-modules OC_MODULES] \\ + [--call-cnv] [--call-sv] [--call-hla] [--call-somatic] [--gatk-germline] \\ + [--open-cravat] [--oc-annotators OC_ANNOTATORS] [--oc-modules OC_MODULES] \\ [--pairs PAIRS] [--pon PANEL_OF_NORMALS] [--wes-mode] [--wes-bed WES_BED] \\ - [--tmp-dir TMP_DIR] [--silent] [--sif-cache SIF_CACHE] \\ + [--skip-qc] [--tmp-dir TMP_DIR] [--silent] [--sif-cache SIF_CACHE] \\ [--singularity-cache SINGULARITY_CACHE] \\ [--resource-bundle RESOURCE_BUNDLE] \\ [--dry-run] [--threads THREADS] \\ @@ -414,6 +414,13 @@ def parsed_arguments(name, description): Options section below for more information about the somatic variant calling pipeline and its options. Example: --call-somatic + + --gatk-germline Call germline variants using GATK4 best pratices. + By default, the pipeline will call germline variants + using deepvariant. If this option is provided, the + pipeline will additionally call germline variants + using GATK4's set of best practices. + Example: --gatk-germline --open-cravat Run OpenCRAVAT to annotate variants. See Annotation Options for more information about what modules are @@ -700,6 +707,17 @@ def parsed_arguments(name, description): help = argparse.SUPPRESS ) + # Call variants using GATK4's + # set of best practices for + # germline variants + subparser_run.add_argument( + '--gatk-germline', + action = 'store_true', + required = False, + default = False, + help = argparse.SUPPRESS + ) + # Skip QC subparser_run.add_argument( '--skip-qc',