diff --git a/bin/parse_influenza_blast_results.py b/bin/parse_influenza_blast_results.py
index c2bdc6c..b8c03d0 100755
--- a/bin/parse_influenza_blast_results.py
+++ b/bin/parse_influenza_blast_results.py
@@ -374,7 +374,7 @@ def report(flu_metadata, blast_results, excel_report, top, pident_threshold,
         ("Release_Date", pl.Categorical),
         ("Genus", pl.Categorical),
         ("Length", pl.UInt16),
-        ("Genotype", pl.Categorical),
+        ("Genotype", str),
         ("Segment", pl.Categorical),
         ("Publications", str),
         ("Geo_Location", pl.Categorical),
diff --git a/conf/modules_illumina.config b/conf/modules_illumina.config
index d6c7c65..e6560a5 100644
--- a/conf/modules_illumina.config
+++ b/conf/modules_illumina.config
@@ -66,4 +66,14 @@ process {
       ]
     ]
   }
+
+  withName: 'SOFTWARE_VERSIONS' {
+   publishDir = [
+     [
+       path: { "${params.outdir}/pipeline_info" },
+       pattern: "software_versions.yml",
+       mode: params.publish_dir_mode
+     ]
+   ]
+ }
 }
diff --git a/modules/local/cat_illumina_fastq.nf b/modules/local/cat_illumina_fastq.nf
index fe62e55..0afe2bd 100644
--- a/modules/local/cat_illumina_fastq.nf
+++ b/modules/local/cat_illumina_fastq.nf
@@ -39,20 +39,21 @@ process CAT_ILLUMINA_FASTQ {
   }
   if (meta.single_end) {
     if (fqList.size >= 1 || fqgzList.size >= 1) {
-      """
-      touch ${prefix}.merged.fastq.gz
-      if [[ ${fqList.size} > 0 ]]; then
-        cat ${readList.join(' ')} | gzip -ck >> ${prefix}.merged.fastq.gz
-      fi
-      if [[ ${fqgzList.size} > 0 ]]; then
-        cat ${readList.join(' ')} >> ${prefix}.merged.fastq.gz
-      fi
+  """
+  touch ${prefix}.merged.fastq.gz
+  if [[ ${fqList.size} > 0 ]]; then
+    cat ${readList.join(' ')} | gzip -ck >> ${prefix}.merged.fastq.gz
+  fi
+  if [[ ${fqgzList.size} > 0 ]]; then
+    cat ${readList.join(' ')} >> ${prefix}.merged.fastq.gz
+  fi
 
-      cat <<-END_VERSIONS > versions.yml
-      "${task.process}":
-        cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
-      END_VERSIONS
-      """
+  cat <<-END_VERSIONS > versions.yml
+  "${task.process}":
+    cat: \$(echo \$(cat --help 2>&1) | sed 's/ (.*//')
+    gzip: \$(echo \$(gzip --help 2>&1) | sed 's/ (.*//')
+  END_VERSIONS
+  """
     }
   } else {
     if (readList.size >= 2) {
@@ -60,43 +61,49 @@ process CAT_ILLUMINA_FASTQ {
       def read1gz = []
       def read2 = []
       def read2gz = []
-      fqList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
-      fqgzList.eachWithIndex{ v, ix -> ( ix & 1 ? read2gz : read1gz ) << v }
-      """
-      # append 1:N:0:. or 2:N:0:. to forward and reverse reads if "[12]:N:.*"
-      # not present in the FASTQ header for compatability with IRMA assembly
-      touch ${prefix}_1.merged.fastq.gz
-      touch ${prefix}_2.merged.fastq.gz
-      if [[ ${read1.size} > 0 ]]; then
-        cat ${read1.join(' ')} \\
-        | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){  chomp \$_; print "\$_ 1:N:0:.\n"; } else { print "\$_"; }' \\
-        | gzip -ck \\
-        >> ${prefix}_1.merged.fastq.gz
-      fi
-      if [[ ${read1gz.size} > 0 ]]; then
-        zcat ${read1gz.join(' ')} \\
-        | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){  chomp \$_; print "\$_ 1:N:0:.\n"; } else { print "\$_"; }' \\
-        | gzip -ck \\
-        >> ${prefix}_1.merged.fastq.gz
-      fi
-      if [[ ${read2.size} > 0 ]]; then
-        cat ${read2.join(' ')} \\
-        | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){  chomp \$_; print "\$_ 2:N:0:.\n"; } else { print "\$_"; }' \\
-        | gzip -ck \\
-        >> ${prefix}_2.merged.fastq.gz
-      fi
-      if [[ ${read2gz.size} > 0 ]]; then
-        zcat ${read2gz.join(' ')} \\
-        | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){  chomp \$_; print "\$_ 2:N:0:.\n"; } else { print "\$_"; }' \\
-        | gzip -ck \\
-        >> ${prefix}_2.merged.fastq.gz
-      fi
+      fqList.eachWithIndex { v, ix -> ( ix & 1 ? read2 : read1 ) << v }
+      fqgzList.eachWithIndex { v, ix -> ( ix & 1 ? read2gz : read1gz ) << v }
+      // append 1:N:0:. or 2:N:0:. to forward and reverse reads if "[12]:N:.*"
+      // not present in the FASTQ header for compatability with IRMA assembly
+"""
+touch ${prefix}_1.merged.fastq.gz
 
-      cat <<-END_VERSIONS > versions.yml
-      "${task.process}":
-        cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
-      END_VERSIONS
-      """
+touch ${prefix}_2.merged.fastq.gz
+
+if [[ ${read1.size} > 0 ]]; then
+  cat ${read1.join(' ')} \\
+  | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){  chomp \$_; print "\$_ 1:N:0:.\n"; } else { print "\$_"; }' \\
+  | gzip -ck \\
+  >> ${prefix}_1.merged.fastq.gz
+fi
+
+if [[ ${read1gz.size} > 0 ]]; then
+  zcat ${read1gz.join(' ')} \\
+  | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){  chomp \$_; print "\$_ 1:N:0:.\n"; } else { print "\$_"; }' \\
+  | gzip -ck \\
+  >> ${prefix}_1.merged.fastq.gz
+fi
+
+if [[ ${read2.size} > 0 ]]; then
+  cat ${read2.join(' ')} \\
+  | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){  chomp \$_; print "\$_ 2:N:0:.\n"; } else { print "\$_"; }' \\
+  | gzip -ck \\
+  >> ${prefix}_2.merged.fastq.gz
+fi
+
+if [[ ${read2gz.size} > 0 ]]; then
+  zcat ${read2gz.join(' ')} \\
+  | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){  chomp \$_; print "\$_ 2:N:0:.\n"; } else { print "\$_"; }' \\
+  | gzip -ck \\
+  >> ${prefix}_2.merged.fastq.gz
+fi
+
+cat <<-END_VERSIONS > versions.yml
+"${task.process}":
+  cat: \$(echo \$(cat --help 2>&1) | sed 's/ (.*//')
+  gzip: \$(echo \$(gzip --help 2>&1) | sed 's/ (.*//')
+END_VERSIONS
+"""
     }
   }
 }
diff --git a/workflows/illumina.nf b/workflows/illumina.nf
index 564f33c..342e6a5 100644
--- a/workflows/illumina.nf
+++ b/workflows/illumina.nf
@@ -78,13 +78,13 @@ workflow ILLUMINA {
   // Credit to nf-core/viralrecon. Source: https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/workflows/illumina.nf#L221
   // Concatenate FastQ files from same sample if required
   CAT_ILLUMINA_FASTQ(ch_input)
-  ch_versions = ch_versions.mix(CAT_ILLUMINA_FASTQ.out.versions)
+  ch_versions = ch_versions.mix(CAT_ILLUMINA_FASTQ.out.versions.first().ifEmpty(null))
 
   IRMA(CAT_ILLUMINA_FASTQ.out.reads, irma_module)
-  ch_versions = ch_versions.mix(IRMA.out.versions)
+  ch_versions = ch_versions.mix(IRMA.out.versions.first().ifEmpty(null))
 
   BLAST_BLASTN(IRMA.out.consensus, BLAST_MAKEBLASTDB.out.db)
-  ch_versions = ch_versions.mix(BLAST_BLASTN.out.versions)
+  ch_versions = ch_versions.mix(BLAST_BLASTN.out.versions.first().ifEmpty(null))
 
   ch_blast = BLAST_BLASTN.out.txt.collect({ it[1] })
   SUBTYPING_REPORT(ZSTD_DECOMPRESS_CSV.out.file, ch_blast)