Fixes #201

nf-core · Jun 10, 2021 · f889766 · f889766
1 parent 5929e12
commit f889766
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Showing 3 changed files with 23 additions and 19 deletions.
diff --git a/main.nf b/main.nf
@@ -47,20 +47,21 @@ WorkflowMain.initialise(workflow, params, log)
 ========================================================================================
 */
 
+include { ILLUMINA } from './workflows/illumina'
+include { NANOPORE } from './workflows/nanopore'
+
 workflow NFCORE_VIRALRECON {
 
     //
     // WORKFLOW: Variant and de novo assembly analysis for Illumina data
     //
     if (params.platform == 'illumina') {
-        include { ILLUMINA } from './workflows/illumina'
         ILLUMINA ()
 
     //
     // WORKFLOW: Variant analysis for Nanopore data
     //
     } else if (params.platform == 'nanopore') {
-        include { NANOPORE } from './workflows/nanopore'
         NANOPORE ()
     }
 }

diff --git a/workflows/illumina.nf b/workflows/illumina.nf
@@ -14,7 +14,9 @@ def valid_params = [
 def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 
 // Validate input parameters
-WorkflowIllumina.initialise(params, log, valid_params)
+if (params.platform == 'illumina') {
+    WorkflowIllumina.initialise(params, log, valid_params)
+}
 
 // Check input path parameters to see if they exist
 def checkPathParamList = [
@@ -691,9 +693,11 @@ workflow ILLUMINA {
 ========================================================================================
 */
 
-workflow.onComplete {
-    NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report, fail_mapped_reads)
-    NfcoreTemplate.summary(workflow, params, log, fail_mapped_reads, pass_mapped_reads)
+if (params.platform == 'illumina') {
+    workflow.onComplete {
+        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report, fail_mapped_reads)
+        NfcoreTemplate.summary(workflow, params, log, fail_mapped_reads, pass_mapped_reads)
+    }
 }
 
 /*

diff --git a/workflows/nanopore.nf b/workflows/nanopore.nf
@@ -12,7 +12,9 @@ def valid_params = [
 def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 
 // Validate input parameters
-WorkflowNanopore.initialise(params, log, valid_params)
+if (params.platform == 'nanopore') {
+    WorkflowNanopore.initialise(params, log, valid_params)
+}
 
 def checkPathParamList = [
     params.input, params.fastq_dir, params.fast5_dir,
@@ -23,6 +25,10 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
 // Stage dummy file to be used as an optional input where required
 ch_dummy_file = file("$projectDir/assets/dummy_file.txt", checkIfExists: true)
 
+// MultiQC config files
+ch_multiqc_config        = file("$projectDir/assets/multiqc_config_nanopore.yaml", checkIfExists: true)
+ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
+
 if (params.input)              { ch_input              = file(params.input)              }
 if (params.fast5_dir)          { ch_fast5_dir          = file(params.fast5_dir)          } else { ch_fast5_dir          = ch_dummy_file     }
 if (params.sequencing_summary) { ch_sequencing_summary = file(params.sequencing_summary) } else { ch_sequencing_summary = ch_multiqc_config }
@@ -35,15 +41,6 @@ if (params.artic_minion_caller == 'medaka') {
     }
 }
 
-/*
-========================================================================================
-    CONFIG FILES
-========================================================================================
-*/
-
-ch_multiqc_config        = file("$projectDir/assets/multiqc_config_nanopore.yaml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
-
 /*
 ========================================================================================
     IMPORT LOCAL MODULES/SUBWORKFLOWS
@@ -511,9 +508,11 @@ workflow NANOPORE {
 ========================================================================================
 */
 
-workflow.onComplete {
-    NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
-    NfcoreTemplate.summary(workflow, params, log)
+if (params.platform == 'nanopore') {
+    workflow.onComplete {
+        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
+        NfcoreTemplate.summary(workflow, params, log)
+    }
 }
 
 /*