Adding gatk-germline cli option

OpenOmics · Jun 10, 2024 · 71627d5 · 71627d5
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diff --git 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
 <sup>**1.**  Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.</sup>  
-<sup>**2.**  Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.</sup>  
+<sup>**2.**  Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.</sup>  
diff --git 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',