Merge pull request #663 from FriederikeHanssen/ascat_controlfreec_ploidy

separate ascat and controlfreec ploidy
nf-core · Jul 20, 2022 · e5a4ffb · e5a4ffb
2 parents e029519 + ea17f5d
commit e5a4ffb
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Showing 4 changed files with 25 additions and 16 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -100,6 +100,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#651](https://github.com/nf-core/sarek/pull/651) - Added TIDDIT_SOMATIC subworkflow
 - [#653](https://github.com/nf-core/sarek/pull/653) - Coherent results subfolder structure between preprocessing, variantcalling and reporting
 - [#659](https://github.com/nf-core/sarek/pull/659) - Update usage.md docu section on `How to run ASCAT with WES`
+- [#663](https://github.com/nf-core/sarek/pull/663) - Add separate parameters for `ASCAT` and `ControlFREEC` back in
 
 ### Fixed
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -794,7 +794,7 @@ process{
                         forcegccontentnormalization: params.wes ? "1" : "0",
                         minimalsubclonepresence: params.wes ? "30" : "20",
                         noisydata: params.wes ? "TRUE" : "FALSE",
-                        ploidy: params.ploidy,
+                        ploidy: params.cf_ploidy,
                         printNA:  params.wes ? "FALSE" : "TRUE",
                         readcountthreshold:  params.wes ? "50" : "10",
                         sex: meta.sex,
@@ -811,7 +811,7 @@ process{
     }
 
     withName: 'FREEC2BED' {
-        ext.args = { "${params.ploidy}" }
+        ext.args = { "${params.cf_ploidy}" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
@@ -820,7 +820,7 @@ process{
     }
 
     withName: 'FREEC2CIRCOS' {
-        ext.args = { "${params.ploidy}" }
+        ext.args = { "${params.cf_ploidy}" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
@@ -829,7 +829,7 @@ process{
     }
 
     withName: 'MAKEGRAPH' {
-        ext.args = { "${params.ploidy}" }
+        ext.args = { "${params.cf_ploidy}" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
@@ -958,7 +958,7 @@ process{
             "gender": meta.sex,
             "genomeVersion": params.ascat_genome,
             "purity": params.ascat_purity,
-            "ploidy": params.ploidy,
+            "ploidy": params.ascat_ploidy,
             "minCounts": params.ascat_min_counts,
             "chrom_names": meta.sex == 'XX' ? "c(1:22, 'X')" : "c(1:22, 'X', 'Y')",
             "min_base_qual": params.ascat_min_base_qual,
@@ -1028,7 +1028,7 @@ process{
                         forcegccontentnormalization: params.wes ? "1" : "0",
                         minimalsubclonepresence: params.wes ? "30" : "20",
                         noisydata: params.wes ? "TRUE" : "FALSE",
-                        ploidy: params.ploidy,
+                        ploidy: params.cf_ploidy,
                         printNA:  params.wes ? "FALSE" : "TRUE",
                         readcountthreshold:  params.wes ? "50" : "10",
                         sex: meta.sex,

diff --git a/nextflow.config b/nextflow.config
@@ -50,11 +50,12 @@ params {
 
     // Variant Calling
     only_paired_variant_calling = false //if true, skips germline variant calling for normal-paired samples
-    ploidy = 2          //null (in ascat, test this works) // Use default value, you can use 2,3,4
+    ascat_ploidy = null                 // default value for ASCAT
     ascat_min_base_qual = 20            // default value for ASCAT
     ascat_min_counts = 10               // default value for ASCAT
     ascat_min_map_qual = 35             // default value for ASCAT
-    ascat_purity = null                 // Use default value
+    ascat_purity = null                 // default value for ASCAT
+    cf_ploidy = 2                       // default value for Control-FREEC
     cf_coeff = 0.05                     // default value for Control-FREEC
     cf_contamination = 0                // default value for Control-FREEC
     cf_contamination_adjustment = false // by default we are not using this in Control-FREEC

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -232,14 +232,6 @@
                     "description": "If true, skips germline variant calling for matched normal to tumor sample. Normal samples without matched tumor will still be processed through germline variant calling tools.",
                     "help_text": "This can speed up computation for somatic variant calling with matched normal samples. If false, all normal samples are processed as well through the germline variantcalling tools. If true, only somatic variant calling is done."
                 },
-                "ploidy": {
-                    "type": "number",
-                    "fa_icon": "fas fa-bacon",
-                    "default": 2,
-                    "description": "Genome ploidy used by ASCAT and ControlFREEC",
-                    "hidden": true,
-                    "help_text": "ControLFREEC: In case of doubt, you can set different values and Control-FREEC will select the one that explains most observed CNAs\n                           Example: ploidy=2 , ploidy=2,3,4\n\nASCAT: optional argument to override ASCAT optimization and supply psi parameter\n(expert parameter, don\u2019t adapt unless you know what you\u2019re doing). See [here](https://raw.githubusercontent.com/VanLoo-lab/ascat/master/man/ASCAT-manual.pdf)"
-                },
                 "ascat_min_base_qual": {
                     "type": "number",
                     "default": 20,
@@ -264,6 +256,13 @@
                     "hidden": true,
                     "help_text": "For more details, see [here](https://raw.githubusercontent.com/VanLoo-lab/ascat/master/man/ASCAT-manual.pdf)."
                 },
+                "ascat_ploidy": {
+                    "type": "string",
+                    "default": null,
+                    "fa_icon": "fas fa-bacon",
+                    "help_text": "ASCAT: optional argument to override ASCAT optimization and supply psi parameter (expert parameter, don\u2019t adapt unless you know what you\u2019re doing). See [here](https://raw.githubusercontent.com/VanLoo-lab/ascat/master/man/ASCAT-manual.pdf)",
+                    "hidden": true
+                },
                 "ascat_purity": {
                     "type": "number",
                     "fa_icon": "fas fa-broom",
@@ -310,6 +309,14 @@
                     "description": "Minimal read coverage for a position to be considered in BAF analysis.",
                     "help_text": "Details, see [ControlFREEC manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html)."
                 },
+                "cf_ploidy": {
+                    "type": "integer",
+                    "default": 2,
+                    "fa_icon": "fas fa-bacon",
+                    "help_text": "In case of doubt, you can set different values and Control-FREEC will select the one that explains most observed CNAs Example: ploidy=2 , ploidy=2,3,4. For more details, see the [manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html).",
+                    "description": "Genome ploidy used by ControlFREEC",
+                    "hidden": true
+                },
                 "cf_window": {
                     "type": "number",
                     "fa_icon": "fas fa-window-maximize",