Merge pull request #28 from jemten/update_gens_args

updates the default args for gens
nf-core · Jun 11, 2024 · 86b516b · 86b516b
2 parents 1aedf57 + d05b1fe
commit 86b516b
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Showing 4 changed files with 19 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,7 @@ Initial release of nf-core/createpanelrefs, created with the [nf-core](https://n
 - [#19](https://github.com/nf-core/createpanelrefs/pull/19) - Updates germlinecnvcaller subworkflow to handle exome samples
 - [#24](https://github.com/nf-core/createpanelrefs/pull/24) - Updates germlinecnvcaller subworkflow to use mappability and segmental duplications track
 - [#24](https://github.com/nf-core/createpanelrefs/pull/24) - Updates germlinecnvcaller and gens subworkflows to use custom names for panel of normals.
+- [#28](https://github.com/nf-core/createpanelrefs/pull/28) - Updates default args for gens subworkflow and made the parameters available from the command line.
 
 ### `Fixed`
 

diff --git a/conf/modules/gens_pon.config b/conf/modules/gens_pon.config
@@ -52,8 +52,8 @@ process {
     }
 
     withName: '.*GENS_PON:GATK4_CREATEREADCOUNTPANELOFNORMALS' {
-        ext.args   = { ["--minimum-interval-median-percentile 10.0",
-                        "--maximum-chunk-size 29349635"].join(" ")}
+        ext.args   = { ["--minimum-interval-median-percentile ${params.gens_min_interval_median_percentile}",
+                        "--maximum-chunk-size ${params.gens_maximum_chunk_size}"].join(" ")}
         publishDir = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/gens_pon/createreadcountpanelofnormals" },

diff --git a/nextflow.config b/nextflow.config
@@ -32,9 +32,11 @@ params {
     gcnv_scatter_content        = 5000
 
     // Gens options
-    gens_bin_length             = 100
-    gens_pon_name               = 'gens'
-    gens_readcount_format       = 'HDF5'
+    gens_bin_length                     = 100
+    gens_maximum_chunk_size             = 167772150
+    gens_min_interval_median_percentile = 5.0
+    gens_pon_name                       = 'gens'
+    gens_readcount_format               = 'HDF5'
 
     // CNVkit options
     cnvkit_targets              = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -127,6 +127,17 @@
                     "fa_icon": "fas fa-sort-numeric-down",
                     "help_text": "Used by GATK's PreprocessIntervals. We recommend a bin length of 100."
                 },
+                "gens_maximum_chunk_size": {
+                    "type": "number",
+                    "default": 167772150,
+                    "description": "Maximum chunk size when writing the HDF5 file"
+                },
+                "gens_min_interval_median_percentile": {
+                    "type": "number",
+                    "default": 5,
+                    "description": "Minimum interval median percentile for gatk CreateReadCountPanelOfNormals",
+                    "help_text": "Genomic intervals with a median (across samples) of fractional coverage (optionally corrected for GC bias) less than or equal to this percentile are filtered out. (This is the first filter applied.)"
+                },
                 "gens_pon_name": {
                     "type": "string",
                     "description": "Name for panel of normals.",