Merge pull request #13 from lescai/hybridcapture

Add optional targets argument to CNVkit. 
note: nf-core lint fails due to template mismatches with current dev.

docs/usage.md

@@ -114,6 +114,24 @@ If you are running the pipeline to generate references for the GATK's germlinecn
 
 <sup>1</sup> To learn more about this file, see [this comment](https://gatk.broadinstitute.org/hc/en-us/community/posts/360074399831/comments/13441240230299) on GATK forum.<br />
 
+### cnvkit
+
+If you are running the pipeline to generate references for the CNVkit variant calling workflow, you should consider that currently the default method for this pipeline is whole-genome. In order to use the CNVkit default, i.e. hybrid capture, when the user is creating a background for targeted capture sequencing (most commonly, exomes or panels), the user should
+
+1. provide an additional config file, in order to change or remove the method specified in the default `ext.args`, i.e.
+
+```
+process {
+
+    withName: CNVKIT_BATCH {
+        ext.args   = {"--output-reference ${meta.id}.cnn"}
+    }
+
+}
+```
+
+2. provide the `--cnvkit_target` parameter (optional) as a .bed file for the targets
+
 ## Core Nextflow arguments
 
 > **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).

nextflow.config

@@ -28,6 +28,9 @@ params {
     scatter_content            = 5000
     segmental_duplications     = null
 
+    // CNVkit options
+    cnvkit_targets             = null
+
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null

nextflow_schema.json

@@ -66,6 +66,17 @@
                 }
             }
         },
+        "cnvkit_options": {
+            "title": "CNVkit options",
+            "type": "object",
+            "description": "Options used by the cnvkit subworkflow",
+            "default": "",
+            "properties": {
+                "cnvkit_targets": {
+                    "type": "string"
+                }
+            }
+        },
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -384,6 +395,9 @@
         {
             "$ref": "#/definitions/germlinecnvcaller_options"
         },
+        {
+            "$ref": "#/definitions/cnvkit_options"
+        },
         {
             "$ref": "#/definitions/input_output_options"
         },

workflows/createpanelrefs.nf

@@ -43,14 +43,16 @@ ch_input = ch_from_samplesheet.map{meta, bam, bai, cram, crai ->
 }
 
 // Initialize file channels based on params, defined in the params.genomes[params.genome] scope
-ch_dict          = params.dict          ? Channel.fromPath(params.dict).map { dict -> [[id:dict.baseName],dict]}.collect()
-                                        : Channel.empty()
-ch_fai           = params.fai           ? Channel.fromPath(params.fai).map { fai -> [[id:fai.baseName],fai]}.collect()
-                                        : Channel.empty()
-ch_fasta         = params.fasta         ? Channel.fromPath(params.fasta).map { fasta -> [[id:fasta.baseName],fasta]}.collect()
-                                        : Channel.empty()
-ch_ploidy_priors = params.ploidy_priors ? Channel.fromPath(params.ploidy_priors).collect()
-                                        : Channel.empty()
+ch_dict           = params.dict           ? Channel.fromPath(params.dict).map { dict -> [[id:dict.baseName],dict]}.collect()
+                                            : Channel.empty()
+ch_fai            = params.fai            ? Channel.fromPath(params.fai).map { fai -> [[id:fai.baseName],fai]}.collect()
+                                            : Channel.empty()
+ch_fasta          = params.fasta          ? Channel.fromPath(params.fasta).map { fasta -> [[id:fasta.baseName],fasta]}.collect()
+                                            : Channel.empty()
+ch_ploidy_priors  = params.ploidy_priors  ? Channel.fromPath(params.ploidy_priors).collect()
+                                            : Channel.empty()
+ch_cnvkit_targets = params.cnvkit_targets ? Channel.fromPath(params.cnvkit_targets).map { targets -> [[id:targets.baseName],targets]}.collect()
+                                            : Channel.value([[:],[]])
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -117,7 +119,7 @@ workflow CREATEPANELREFS {
         .map {meta, bam -> [ meta, [], bam ]}
         .set { ch_cnvkit_input }
 
-        CNVKIT_BATCH ( ch_cnvkit_input, ch_fasta, [[:],[]], [[:],[]], [[:],[]], true )
+        CNVKIT_BATCH ( ch_cnvkit_input, ch_fasta, [[:],[]], ch_cnvkit_targets, [[:],[]], true )
         ch_versions = ch_versions.mix(CNVKIT_BATCH.out.versions)
     }