diff --git a/subworkflows/local/hic_mapping.nf b/subworkflows/local/hic_mapping.nf
index 1ee3451a..1c910cf6 100755
--- a/subworkflows/local/hic_mapping.nf
+++ b/subworkflows/local/hic_mapping.nf
@@ -30,14 +30,14 @@ workflow HIC_MAPPING {
     take:
     reference_tuple     // Channel [ val(meta), path(file) ]
     reference_index     // Channel [ val(meta), path(file) ]
-    dot_genome          // Channel [ val(meta), [ datafile ]]
+    dot_genome          // Channel [ val(meta), [ datafile ] ]
     hic_reads_path      // Channel [ val(meta), path(directory) ]
-    gap_file
-    coverage_file
-    logcoverage_file
-    telo_file
-    repeat_density_file
-    workflow_setting    // val( {RAPID | FULL } )
+    gap_file            // Channel [ val(meta), path(file) ]
+    coverage_file       // Channel [ val(meta), path(file) ]
+    logcoverage_file    // Channel [ val(meta), path(file) ]
+    telo_file           // Channel [ val(meta), path(file) ]
+    repeat_density_file // Channel [ val(meta), path(file) ]
+    workflow_setting    // val( { RAPID | FULL } )
 
     main:
     ch_versions         = Channel.empty()
diff --git a/workflows/treeval.nf b/workflows/treeval.nf
index 98b11dbb..da30e595 100755
--- a/workflows/treeval.nf
+++ b/workflows/treeval.nf
@@ -238,7 +238,6 @@ workflow TREEVAL {
         GENERATE_GENOME.out.ref_index,
         GENERATE_GENOME.out.dot_genome,
         YAML_INPUT.out.hic_reads,
-        YAML_INPUT.out.assembly_id,
         GAP_FINDER.out.gap_file,
         LONGREAD_COVERAGE.out.ch_covbw_nor,
         LONGREAD_COVERAGE.out.ch_covbw_log,
diff --git a/workflows/treeval_rapid.nf b/workflows/treeval_rapid.nf
index e4654888..c264cb1c 100755
--- a/workflows/treeval_rapid.nf
+++ b/workflows/treeval_rapid.nf
@@ -64,67 +64,65 @@ workflow TREEVAL_RAPID {
     // SUBWORKFLOW: Takes input fasta file and sample ID to generate a my.genome file
     //
     GENERATE_GENOME (
-        YAML_INPUT.out.assembly_id,
         YAML_INPUT.out.reference
     )
-    ch_versions     = ch_versions.mix(GENERATE_GENOME.out.versions)
+    ch_versions     = ch_versions.mix( GENERATE_GENOME.out.versions )
 
     //
     // SUBWORKFLOW: GENERATES A BIGWIG FOR A REPEAT DENSITY TRACK
     //
     REPEAT_DENSITY (
-        GENERATE_GENOME.out.reference_tuple,
+        YAML_INPUT.out.reference,
         GENERATE_GENOME.out.dot_genome
     )
-    ch_versions     = ch_versions.mix(REPEAT_DENSITY.out.versions)
+    ch_versions     = ch_versions.mix( REPEAT_DENSITY.out.versions )
 
     //
     // SUBWORKFLOW: GENERATES A GAP.BED FILE TO ID THE LOCATIONS OF GAPS
     //
     GAP_FINDER (
-        GENERATE_GENOME.out.reference_tuple,
+        YAML_INPUT.out.reference,
         GENERATE_GENOME.out.max_scaff_size
     )
-    ch_versions     = ch_versions.mix(GAP_FINDER.out.versions)
+    ch_versions     = ch_versions.mix( GAP_FINDER.out.versions )
 
     //
     // SUBWORKFLOW: GENERATE TELOMERE WINDOW FILES WITH PACBIO READS AND REFERENCE
     //
     TELO_FINDER (
         GENERATE_GENOME.out.max_scaff_size,
-        GENERATE_GENOME.out.reference_tuple,
+        YAML_INPUT.out.reference,
         YAML_INPUT.out.teloseq
     )
-    ch_versions     = ch_versions.mix(TELO_FINDER.out.versions)
+    ch_versions     = ch_versions.mix( TELO_FINDER.out.versions )
 
     //
     // SUBWORKFLOW: Takes reference, pacbio reads
     //
     LONGREAD_COVERAGE (
-        GENERATE_GENOME.out.reference_tuple,
+        YAML_INPUT.out.reference,
         GENERATE_GENOME.out.dot_genome,
         YAML_INPUT.out.pacbio_reads
     )
-    ch_versions     = ch_versions.mix(LONGREAD_COVERAGE.out.versions)
+    ch_versions     = ch_versions.mix( LONGREAD_COVERAGE.out.versions )
 
     //
     // SUBWORKFLOW: Takes reads and assembly, produces kmer plot
     //
     KMER (
-        GENERATE_GENOME.out.reference_tuple,
+        YAML_INPUT.out.reference,
         YAML_INPUT.out.pacbio_reads
     )
-    ch_versions     = ch_versions.mix(KMER.out.versions)
+    ch_versions     = ch_versions.mix( KMER.out.versions )
 
     //
     // SUBWORKFLOW: GENERATE HIC MAPPING TO GENERATE PRETEXT FILES AND JUICEBOX
     //
     HIC_MAPPING (
-        GENERATE_GENOME.out.reference_tuple,
+        YAML_INPUT.out.reference,
         GENERATE_GENOME.out.ref_index,
         GENERATE_GENOME.out.dot_genome,
         YAML_INPUT.out.hic_reads,
-        YAML_INPUT.out.assembly_id,
         GAP_FINDER.out.gap_file,
         LONGREAD_COVERAGE.out.ch_covbw_nor,
         LONGREAD_COVERAGE.out.ch_covbw_log,