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',