Update happy module

docs/usage.md

@@ -38,8 +38,9 @@ You can specify your truth data using the following parameters:
 
 - `--truth_vcf`: The path to the gold standard truth VCF file. This file contains the validated variants that your test sets will be evaluated against.
 - `--truth_id`: The sample name exactly as it appears inside the truth VCF header. This is a critical parameter because tools like RTG Tools and VCF subtraction steps require the exact sample ID to correctly parse the genotypes.
-- `--regions_bed`: A BED file defining the high confidence regions of the genome such as the Genome in a Bottle confident regions. The benchmarking tools will restrict their evaluation to only the variants that fall within these defined coordinates. This ensures that complex or unmappable regions do not artificially skew your performance metrics.
-- `--targets_bed`: The path to the BED file containing your assay target regions. When you provide this file the pipeline will automatically intersect it with your truth confident regions (provided via the regions bed parameter). This creates a final specific evaluation area that ensures you are only benchmarking variants within your actual sequencing target space.
+- `--falsepositive_bed`: A BED file defining the high-confidence regions of the genome (e.g., Genome in a Bottle confident beds). Called variants NOT in `truth_vcf` but WITHIN `falsepositive_bed` will be counted as FP.
+- `--regions_bed`: A BED file for restricting analysis in specific regions of interest. The benchmarking tools will restrict their evaluation to only the variants that fall within these defined coordinates.
+- `--targets_bed`: Use that param only if you want to pass the regions of interest through the [-T argument](https://github.com/Illumina/hap.py/blob/master/doc/happy.md#restricting-to-subsets-of-the-genome) for `sompy` and `happy`. This is primarily used for dense regions of interest, such as exome data. The same file will be passed to `vcfeval` using its `--bed-regions` argument.
 
 ## Stratification Files
 

modules.json

@@ -82,7 +82,7 @@
                     },
                     "happy/happy": {
                         "branch": "master",
-                        "git_sha": "4020dbe4bb4a7d71be85bf8f77dbdf6c06fa401f",
+                        "git_sha": "59697ca2f109700926f11a1718efcb3ce5b99ed4",
                         "installed_by": ["modules"]
                     },
                     "happy/prepy": {

nextflow_schema.json

@@ -78,7 +78,7 @@
                     "format": "file-path",
                     "exists": true,
                     "pattern": "^\\S+\\.(bed)?(\\.gz)?$",
-                    "description": "Path to false positive BED. Only applicable to happy and sompy tool.",
+                    "description": "Path to false positive / confident call regions BED. Only applicable for happy and sompy.",
                     "help_text": "Falsepositive BED files",
                     "fa_icon": "fas fa-file-csv"
                 },