Add skip_clean if type=HiFi to avoid db download

Add check SR parameters

main_dsl2.nf

@@ -23,7 +23,7 @@ include { DATABASES } from './subworkflows/00_databases'
      Options:
      
      01_clean_qc options:
-       --skip_01_clean_qc            Skip 01_clean_qc step.
+       --skip_clean            Skip 01_clean_qc step.
        --adapter1                    Sequence of adapter 1. Default: Illumina TruSeq adapter.
        --adapter2                    Sequence of adapter 2. Default: Illumina TruSeq adapter.
        --skip_sickle                 Skip sickle process.
@@ -72,6 +72,13 @@ include { DATABASES } from './subworkflows/00_databases'
    """.stripIndent()
  }
 
+// Show help message.
+
+if (params.help){
+  helpMessage()
+  exit 0
+}
+
 
 def getAndCheckHeader() {
     File file = new File(params.input)
@@ -115,12 +122,29 @@ workflow {
 
 
 // Check mandatory parameters
+
 ////////////
 // Start check samplesheet
 ////////////
 if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
 
+skip_clean = params.skip_clean
 
+if (params.type == 'SR') {
+    if (!['metaspades','megahit'].contains(params.assembly)){
+    exit 1, "Invalid short read aligner option: ${params.assembly}. Valid options: 'metaspades', 'megahit'"
+  }
+  if (!["solexa","illumina","sanger"].contains(params.quality_type)){
+    exit 1, "Invalid quality_type option: ${params.quality_type}. Valid options:'solexa','illumina','sanger'"
+  }
+  if (!(params.skip_removal_host) && !(params.host_fasta) && !(params.skip_clean)) {
+    exit 1, "You must specify --host_fasta or skip cleaning host step with option --skip_removal_host or skip all clean and qc modules with --skip_clean"
+  }
+}
+else {
+  skip_clean = true
+}
+println(params)
 header = getAndCheckHeader()
 
 Channel.from(file(params.input)
@@ -142,12 +166,14 @@ Channel.from(file(params.input)
         } 
     .set  { ch_inputs }
         
-ch_inputs.view { it -> "FF ${it} " }
+
+
+
 ////////////
 // End check samplesheet  
 ////////////
 
-  DATABASES ()
+  DATABASES (skip_clean)
   ch_kaiju_db = DATABASES.out.kaiju_db
   ch_eggnog_db = DATABASES.out.eggnog
   ch_taxonomy = DATABASES.out.taxonomy

subworkflows/00_databases.nf

 workflow DATABASES {
+    take :
+        skip_clean
     main:
         ch_kaiju_db = Channel.empty()
-        if (!params.skip_clean && !params.skip_kaiju) { //kaiju_db
+        if (!skip_clean && !params.skip_kaiju) { //kaiju_db
             if (!params.kaiju_db_dir && params.kaiju_db_url) {
-                INDEX_KAIJU(params.kaiju_db)
-                ch_kaiju_db = INDEX_KAIJU.out.kaiju_db
+                println("INDEX_KAIJU")
+                INDEX_KAIJU(params.kaiju_db_url)
+                ch_kaiju_db = INDEX_KAIJU.out.kaiju_db_dir
             } else if (params.kaiju_db_dir) {
                 if (file(params.kaiju_db_dir + "/kaiju_db*.fmi").size == 1) {
                     println("Creating kaiju_db channel")