Fix merge cockup

.github/workflows/ci.yml

@@ -41,7 +41,7 @@ jobs:
           - "--shortread_complexityfilter_tool prinseq"
           - "--perform_runmerging"
           - "--perform_runmerging --shortread_clipmerge_mergepairs"
-          - "--shortread_complexityfilter false --shortread_hostremoval"
+          - "--shortread_complexityfilter false --perform_shortread_hostremoval"
 
     steps:
       - name: Check out pipeline code

conf/test.config

@@ -31,6 +31,6 @@ params {
     perform_shortread_clipmerge           = true
     perform_longread_clip                 = false
     perform_shortread_complexityfilter    = true
-    shortread_hostremoval           = true
+    perform_shortread_hostremoval           = true
     shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
 }

nextflow.config

@@ -81,7 +81,7 @@ params {
     save_runmerged_reads        = false
 
     // Host Removal
-    shortread_hostremoval           = false
+    perform_shortread_hostremoval           = false
     shortread_hostremoval_reference = null
     shortread_hostremoval_index     = null
 

nextflow_schema.json

@@ -359,7 +359,7 @@
         "perform_runmerging": {
             "type": "boolean"
         },
-        "shortread_hostremoval": {
+        "perform_shortread_hostremoval": {
             "type": "boolean"
         },
         "shortread_hostremoval_reference": {

workflows/taxprofiler.nf

@@ -22,11 +22,10 @@ if (params.databases) { ch_databases = file(params.databases) } else { exit 1, '
 if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
 if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "[nf-core/taxprofiler] error: cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
 
-// TODO Add check if index but no reference exit 1
+if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
-if (params.shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
 if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
 
-if (params.shortread_hostremoval_reference ) { ch_reference       = file(params.shortread_hostremoval_reference) } else { ch_reference       = [] }
+if (params.shortread_hostremoval_reference ) { ch_reference       = file(params.shortread_hostremoval_reference) }
 if (params.shortread_hostremoval_index     ) { ch_reference_index = file(params.shortread_hostremoval_index    ) } else { ch_reference_index = [] }
 
 /*
@@ -140,15 +139,13 @@ workflow TAXPROFILER {
         SUBWORKFLOW: HOST REMOVAL
     */
 
-    if ( params.shortread_hostremoval ) {
+    if ( params.perform_shortread_hostremoval ) {
         ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads
         ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions.first())
     } else {
         ch_shortreads_hostremoved = ch_shortreads_filtered
     }
 
-    */
-
     if ( params.perform_runmerging ) {
 
         ch_reads_for_cat_branch = ch_shortreads_hostremoved
@@ -225,11 +222,11 @@ workflow TAXPROFILER {
         ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
     }
 
-    if (params.shortread_hostremoval) {
+    if (params.perform_shortread_hostremoval) {
         ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
         ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
     }
-    
+
     if (params.perform_runmerging){
         ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
     }