Assembly QC -> return the unmodified contigs if no contigs decontamin…

…ation is used.

subworkflows/local/assembly_qc.nf

@@ -39,7 +39,7 @@ workflow ASSEMBLY_QC {
         contaminated_contigs = BLAST_BLASTN_HUMAN_PHIX.out.txt
     }
 
-    if ( host_reference_genome != null) {
+    if ( host_reference_genome != null ) {
 
         ch_blast_host_refs = Channel.fromPath( "${params.blast_reference_genomes_folder}/${host_reference_genome}*", checkIfExists: true)
             .collect().map {
@@ -53,20 +53,25 @@ workflow ASSEMBLY_QC {
 
         ch_versions = ch_versions.mix(BLAST_BLASTN_HOST.out.versions.first())
 
-        contaminated_contigs = BLAST_BLASTN_HUMAN_PHIX.out.txt.mix( BLAST_BLASTN_HOST.out.txt )
-    } else {
-        contaminated_contigs = BLAST_BLASTN_HUMAN_PHIX.out.txt
+        contaminated_contigs = contaminated_contigs.mix( BLAST_BLASTN_HOST.out.txt )
     }
 
-    // TODO: this is not fit for samplesheets kind of inputs
+    // TODO: this is not fit for samplesheets kind of inputs, it should .join with the contaminated contigs channel
     SEQKIT_GREP(
         SEQKIT_SEQ.out.fastx,
         contaminated_contigs.map { meta, hits_txt -> { hits_txt }}.collectFile(name: "contaminated_contigs.txt", newLine: true)
     )
 
+    if ( !params.remove_human_phix && host_reference_genome == null ) {
+        // No decontamination //
+        filtered_contigs = assembly
+    } else {
+        filtered_contigs = SEQKIT_GREP.out.filter
+    }
+
     ch_versions = ch_versions.mix(SEQKIT_GREP.out.versions)
 
     emit:
-    filtered_contigs = SEQKIT_GREP.out.filter
+    filtered_contigs = filtered_contigs
     versions         = ch_versions
 }