diff --git a/conf/modules.config b/conf/modules.config
index 632fa69..5cdc4e9 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -197,6 +197,20 @@ process {
             '-outfmt',
             '"6 qseqid ppos"',
         ].join(' ').trim()
+
+        publishDir = [
+            [
+                path: "${params.outdir}",
+                mode: params.publish_dir_mode,
+                failOnError: true,
+                saveAs: {
+                    filename -> {
+                        def output_file = new File(filename);
+                        return "${study_reads_folder()}/assembly/${meta.assembler}/${meta.assembler_version}/decontamination/${output_file.name}";
+                    }
+                }
+            ]
+        ]
     }
 
     withName: 'SEQKIT_GREP' {
@@ -319,24 +333,4 @@ process {
         // NOTICE: Maximum number of references (--max-ref-number) is set to 0, search in SILVA 16S rRNA database is disabled //
         ext.args = "--max-ref-num 0"
     }
-
-    withName: 'PUBLISH_DECONTAMINATED' {
-        cpus   = { check_max( 1                    , 'cpus'    ) }
-        memory = { check_max( 250.MB * task.attempt, 'memory'  ) }
-        time   = { check_max( 30.m                 , 'time'    ) }
-
-        publishDir = [
-            [
-                path: "${params.outdir}",
-                mode: params.publish_dir_mode,
-                failOnError: true,
-                saveAs: {
-                    filename -> {
-                        def output_file = new File(filename);
-                        return "${study_reads_folder()}/assembly/${meta.assembler}/${meta.assembler_version}/decontamination/${output_file.name}";
-                    }
-                }
-            ]
-        ]
-    }
 }
diff --git a/modules/local/publish_decontaminated.nf b/modules/local/publish_decontaminated.nf
deleted file mode 100644
index c57383b..0000000
--- a/modules/local/publish_decontaminated.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-process PUBLISH_DECONTAMINATED {
-
-    input:
-    tuple val(meta), path(decontaminated_contigs)
-
-    output:
-    path("${meta.id}_decontaminated_contigs.txt")
-
-    script:
-    """
-    mv ${decontaminated_contigs} ${meta.id}_decontaminated_contigs.txt
-    """
-}
diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf
index 2613e54..9b44592 100644
--- a/modules/nf-core/blast/blastn/main.nf
+++ b/modules/nf-core/blast/blastn/main.nf
@@ -20,7 +20,7 @@ process BLAST_BLASTN {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta2.id}"
     def is_compressed = fasta.getExtension() == "gz" ? true : false
     def fasta_name = is_compressed ? fasta.getBaseName() : fasta
 
diff --git a/subworkflows/local/assembly_qc.nf b/subworkflows/local/assembly_qc.nf
index a4cdc02..c81beb0 100644
--- a/subworkflows/local/assembly_qc.nf
+++ b/subworkflows/local/assembly_qc.nf
@@ -2,7 +2,6 @@ include { BLAST_BLASTN as BLAST_BLASTN_HUMAN_PHIX } from '../../modules/nf-core/
 include { BLAST_BLASTN as BLAST_BLASTN_HOST       } from '../../modules/nf-core/blast/blastn/main'
 include { SEQKIT_GREP                             } from '../../modules/nf-core/seqkit/grep/main'
 include { SEQKIT_SEQ                              } from '../../modules/nf-core/seqkit/seq/main'
-include { PUBLISH_DECONTAMINATED                  } from '../../modules/local/publish_decontaminated'
 
 workflow ASSEMBLY_QC {
 
@@ -40,7 +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 {
@@ -54,23 +53,25 @@ workflow ASSEMBLY_QC {
 
         ch_versions = ch_versions.mix(BLAST_BLASTN_HOST.out.versions.first())
 
-        contaminated_contigs = Channel.of( BLAST_BLASTN_HUMAN_PHIX.out.txt, BLAST_BLASTN_HOST.out.txt )
-            .collectFile(name: "contaminated_contigs_host.txt", newLine: true)
-    } else {
-        contaminated_contigs = BLAST_BLASTN_HUMAN_PHIX.out.txt
+        contaminated_contigs = contaminated_contigs.mix( BLAST_BLASTN_HOST.out.txt )
     }
 
-    // TODO: this process only function is to publish the decontaminated contigs txt file
-    PUBLISH_DECONTAMINATED( contaminated_contigs )
-
+    // 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 }}
+        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
 }
diff --git a/tests/main.nf.test b/tests/main.nf.test
index 54fd341..821dfa0 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_pipeline {
                 assert success
                 assert trace.succeeded().count{ task -> task.name.contains("SPADES") } == 1
                 assert trace.succeeded().count{ task -> task.name.contains("MEGAHIT") } == 0
-                assert trace.succeeded().size() == 17
+                assert trace.succeeded().size() == 16
             }
         }
 
@@ -45,7 +45,7 @@ nextflow_pipeline {
                 assert success
                 assert trace.succeeded().count{ task -> task.name.contains("SPADES") } == 0
                 assert trace.succeeded().count{ task -> task.name.contains("MEGAHIT") } == 1
-                assert trace.tasks().size() == 17
+                assert trace.tasks().size() == 16
             }
         }
 
@@ -111,7 +111,7 @@ nextflow_pipeline {
                 assert success
                 assert trace.succeeded().count{ task -> task.name.contains("SPADES") } == 0
                 assert trace.succeeded().count{ task -> task.name.contains("MEGAHIT") } == 1
-                assert trace.tasks().size() == 17
+                assert trace.tasks().size() == 16
             }
         }