diff --git a/modules/local/poppunk/createdb/main.nf b/modules/local/poppunk/createdb/main.nf
index e41d9a25..3239abbb 100644
--- a/modules/local/poppunk/createdb/main.nf
+++ b/modules/local/poppunk/createdb/main.nf
@@ -9,6 +9,7 @@ process POPPUNK_CREATEDB {
     input:
 
     path filesheet
+    path assemblies
 
     output:
 
diff --git a/modules/local/ppanggolin/workflow/main.nf b/modules/local/ppanggolin/workflow/main.nf
index 462c0c75..7ba66c5a 100644
--- a/modules/local/ppanggolin/workflow/main.nf
+++ b/modules/local/ppanggolin/workflow/main.nf
@@ -11,6 +11,7 @@ process PPANGGOLIN_WORKFLOW {
 
     input:
     tuple val(meta), path(samplesheet)
+    path gffs
 
     output:
     tuple val(meta), path("$prefix")             , emit: results
diff --git a/modules/nf-core/panaroo/run/main.nf b/modules/nf-core/panaroo/run/main.nf
index 7947fc53..d1cfcb8c 100644
--- a/modules/nf-core/panaroo/run/main.nf
+++ b/modules/nf-core/panaroo/run/main.nf
@@ -9,6 +9,7 @@ process PANAROO_RUN {
 
     input:
     tuple val(meta), path(gff)
+    path gffs
 
     output:
     tuple val(meta), path("results/*")                                      , emit: results
diff --git a/subworkflows/local/phylo.nf b/subworkflows/local/phylo.nf
index b7bfea4d..06caa9c6 100755
--- a/subworkflows/local/phylo.nf
+++ b/subworkflows/local/phylo.nf
@@ -26,7 +26,7 @@ workflow PHYLOGENOMICS{
         ch_software_versions = Channel.empty()
 
         gffs
-            .map { meta, path -> [meta.id, path.toString()] }
+            .map { meta, path -> [meta.id, path.getName()] }
             .set { gff_paths }
 
         // Create samplesheet
@@ -39,7 +39,7 @@ workflow PHYLOGENOMICS{
                 .map{ path -> [[id: 'ppanggolin'], path] }
                 .set { gff_samplesheet }
 
-            PPANGGOLIN_WORKFLOW(gff_samplesheet)
+            PPANGGOLIN_WORKFLOW(gff_samplesheet, gffs.collect{ it[1] })
 
             PPANGGOLIN_WORKFLOW.out.pangenome.set { pangenome }
 
@@ -76,7 +76,7 @@ workflow PHYLOGENOMICS{
             * Core gene identification and alignment
             */
             // By default, run panaroo
-            PANAROO_RUN(gff_samplesheet)
+            PANAROO_RUN(gff_samplesheet, gffs.collect{ it[1] })
             PANAROO_RUN.out.aln.collect{ meta, aln -> aln }.set{ ch_core_alignment }
             PANAROO_RUN.out.accessory_aln.set{ ch_all_alignments }
 
diff --git a/subworkflows/local/poppunk.nf b/subworkflows/local/poppunk.nf
index 7f7a6237..64e14563 100644
--- a/subworkflows/local/poppunk.nf
+++ b/subworkflows/local/poppunk.nf
@@ -24,14 +24,14 @@ workflow RUN_POPPUNK {
         }
 
         genome_assemblies
-            .map { meta, path -> [meta.id, path.toString()] }
+            .map { meta, path -> [meta.id, path.getName()] }
             .collectFile(newLine: true) { item ->
                 [ "${item[0]}.txt", item[0] + '\t' + item[1] ]
             }
             .collectFile(name: 'poppunk_samplesheet.tsv')
             .set { poppunk_samplesheet }
 
-        POPPUNK_CREATEDB(poppunk_samplesheet)
+        POPPUNK_CREATEDB(poppunk_samplesheet, genome_assemblies.collect { it[1] } )
 
         POPPUNK_CREATEDB.out.poppunk_db.set { poppunk_db }
 
diff --git a/tests/subworkflows/local/phylo.nf.test b/tests/subworkflows/local/phylo.nf.test
index a4b54e73..ef556f45 100644
--- a/tests/subworkflows/local/phylo.nf.test
+++ b/tests/subworkflows/local/phylo.nf.test
@@ -15,9 +15,9 @@ nextflow_workflow {
                 """
                 // define inputs of the workflow here. Example:
                 input[0] = Channel.of(
-                    [[id:'SRR14022735'], '$baseDir/test/SRR14022735_T1.gff'],
-                    [[id:'SRR14022764'], '$baseDir/test/SRR14022764_T1.gff'],
-                    [[id:'SRR14022754'], '$baseDir/test/SRR14022754_T1.gff']
+                    [[id:'SRR14022735'], file('$baseDir/test/SRR14022735_T1.gff')],
+                    [[id:'SRR14022764'], file('$baseDir/test/SRR14022764_T1.gff')],
+                    [[id:'SRR14022754'], file('$baseDir/test/SRR14022754_T1.gff')]
                 )
                 // Don't use full alignment
                 input[1] = false
diff --git a/tests/subworkflows/local/poppunk.nf.test.skip b/tests/subworkflows/local/poppunk.nf.test.skip
index e9ea2386..00bd5028 100644
--- a/tests/subworkflows/local/poppunk.nf.test.skip
+++ b/tests/subworkflows/local/poppunk.nf.test.skip
@@ -15,10 +15,10 @@ nextflow_workflow {
                 """
                 // define inputs of the workflow here. Example:
                 input[0] = Channel.of(
-                    [[id:'SRR14022735'], "$baseDir/test/SRR14022735_T1.scaffolds.fa"],
-                    [[id:'SRR14022737'], "$baseDir/test/SRR14022737_T1.scaffolds.fa"],
-                    [[id:'SRR14022754'], "$baseDir/test/SRR14022754_T1.scaffolds.fa"],
-                    [[id:'SRR14022764'], "$baseDir/test/SRR14022764_T1.scaffolds.fa"],
+                    [[id:'SRR14022735'], file("$baseDir/test/SRR14022735_T1.scaffolds.fa")],
+                    [[id:'SRR14022737'], file("$baseDir/test/SRR14022737_T1.scaffolds.fa")],
+                    [[id:'SRR14022754'], file("$baseDir/test/SRR14022754_T1.scaffolds.fa")],
+                    [[id:'SRR14022764'], file("$baseDir/test/SRR14022764_T1.scaffolds.fa")],
                 )
                 """
             }