Check for needed reference only

CHANGELOG.md

@@ -12,12 +12,16 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 -   [#744](https://github.com/SciLifeLab/Sarek/pull/744) - Refactor `germlineVC.nf`
 
 ### `Added`
+
 -   [#753](https://github.com/SciLifeLab/Sarek/pull/753) - Update `binac`, `cfc` configuration
 
 ### `Fixed`
+
 -   [#749](https://github.com/SciLifeLab/Sarek/pull/749) - Fix config problematic use of queue `core` for uppmax-slurm
 -   [#751](https://github.com/SciLifeLab/Sarek/pull/751), [#756](https://github.com/SciLifeLab/Sarek/pull/756) - Typos in `igenomes.config`
 -   [#757](https://github.com/SciLifeLab/Sarek/pull/757) - Typos in `binac`, `cfc` configuration
+-   [#758](https://github.com/SciLifeLab/Sarek/pull/758) - Typos in `ASCAT` documentation
+-   [#765](https://github.com/SciLifeLab/Sarek/pull/765) - Check only for references that are needed to fix [#754](https://github.com/SciLifeLab/Sarek/issues/754)
 
 ## [2.3.FIX1] - 2019-03-04
 

germlineVC.nf

@@ -51,11 +51,11 @@ if (workflow.profile == 'awsbatch') {
 
 tools = params.tools ? params.tools.split(',').collect{it.trim().toLowerCase()} : []
 
-referenceMap = defineReferenceMap()
 toolList = defineToolList()
+if (!SarekUtils.checkParameterList(tools,toolList)) exit 1, 'Unknown tool(s), see --help for more information'
 
+referenceMap = defineReferenceMap(tools)
 if (!SarekUtils.checkReferenceMap(referenceMap)) exit 1, 'Missing Reference file(s), see --help for more information'
-if (!SarekUtils.checkParameterList(tools,toolList)) exit 1, 'Unknown tool(s), see --help for more information'
 
 if (params.test && params.genome in ['GRCh37', 'GRCh38']) {
   referenceMap.intervals = file("$workflow.projectDir/repeats/tiny_${params.genome}.list")
@@ -454,20 +454,22 @@ def checkUppmaxProject() {
   return !(workflow.profile == 'slurm' && !params.project)
 }
 
-def defineReferenceMap() {
+def defineReferenceMap(tools) {
   if (!(params.genome in params.genomes)) exit 1, "Genome ${params.genome} not found in configuration"
-  return [
-    'dbsnp'            : checkParamReturnFile("dbsnp"),
-    'dbsnpIndex'       : checkParamReturnFile("dbsnpIndex"),
-    // genome reference dictionary
-    'genomeDict'       : checkParamReturnFile("genomeDict"),
-    // FASTA genome reference
+  def referenceMap =
+  [
     'genomeFile'       : checkParamReturnFile("genomeFile"),
-    // genome .fai file
     'genomeIndex'      : checkParamReturnFile("genomeIndex"),
-    // intervals file for spread-and-gather processes
     'intervals'        : checkParamReturnFile("intervals")
   ]
+  if ('haplotypecaller' in tools) {
+    referenceMap.putAll(
+      'dbsnp'            : checkParamReturnFile("dbsnp"),
+      'dbsnpIndex'       : checkParamReturnFile("dbsnpIndex"),
+      'genomeDict'       : checkParamReturnFile("genomeDict")
+    )
+  }
+  return referenceMap
 }
 
 def defineToolList() {

somaticVC.nf

@@ -58,11 +58,11 @@ if (workflow.profile == 'awsbatch') {
 
 tools = params.tools ? params.tools.split(',').collect{it.trim().toLowerCase()} : []
 
-referenceMap = defineReferenceMap()
 toolList = defineToolList()
+if (!SarekUtils.checkParameterList(tools,toolList)) exit 1, 'Unknown tool(s), see --help for more information'
 
+referenceMap = defineReferenceMap(tools)
 if (!SarekUtils.checkReferenceMap(referenceMap)) exit 1, 'Missing Reference file(s), see --help for more information'
-if (!SarekUtils.checkParameterList(tools,toolList)) exit 1, 'Unknown tool(s), see --help for more information'
 
 if (params.test && params.genome in ['GRCh37', 'GRCh38']) {
   referenceMap.intervals = file("$workflow.projectDir/repeats/tiny_${params.genome}.list")
@@ -748,23 +748,28 @@ def checkUppmaxProject() {
   return !(workflow.profile == 'slurm' && !params.project)
 }
 
-def defineReferenceMap() {
+def defineReferenceMap(tools) {
   if (!(params.genome in params.genomes)) exit 1, "Genome ${params.genome} not found in configuration"
-  return [
-    // loci file for ascat
-    'acLoci'           : checkParamReturnFile("acLoci"),
-    'acLociGC'           : checkParamReturnFile("acLociGC"),
-    'dbsnp'            : checkParamReturnFile("dbsnp"),
-    'dbsnpIndex'       : checkParamReturnFile("dbsnpIndex"),
-    // genome reference dictionary
+  def referenceMap =
+  [
     'genomeDict'       : checkParamReturnFile("genomeDict"),
-    // FASTA genome reference
     'genomeFile'       : checkParamReturnFile("genomeFile"),
-    // genome .fai file
     'genomeIndex'      : checkParamReturnFile("genomeIndex"),
-    // intervals file for spread-and-gather processes
     'intervals'        : checkParamReturnFile("intervals")
   ]
+  if ('ascat' in tools) {
+    referenceMap.putAll(
+      'acLoci'           : checkParamReturnFile("acLoci"),
+      'acLociGC'         : checkParamReturnFile("acLociGC")
+    )
+  }
+  if ('mutect2' in tools) {
+    referenceMap.putAll(
+      'dbsnp'            : checkParamReturnFile("dbsnp"),
+      'dbsnpIndex'       : checkParamReturnFile("dbsnpIndex")
+    )
+  }
+  return referenceMap
 }
 
 def defineToolList() {