From 622be5e323d630dc45df02ccdc4d53cf298c7058 Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Mon, 7 Oct 2024 16:42:14 +0000
Subject: [PATCH 01/13] Initial commit for TheiaEuk ONT

---
 .dockstore.yml                          |   5 ++
 workflows/theiaeuk/wf_theiaeuk_ont.wdl  | 108 ++++++++++++++++++++++++
 workflows/utilities/wf_merlin_magic.wdl |  56 ++++++++----
 3 files changed, 153 insertions(+), 16 deletions(-)
 create mode 100644 workflows/theiaeuk/wf_theiaeuk_ont.wdl

diff --git a/.dockstore.yml b/.dockstore.yml
index 5306d30ed..21f1b57ce 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -5,6 +5,11 @@ workflows:
    primaryDescriptorPath: /workflows/theiaeuk/wf_theiaeuk_illumina_pe.wdl
    testParameterFiles:
     - /tests/inputs/empty.json
+ - name: TheiaEuk_ONT_PHB
+   subclass: WDL
+   primaryDescriptorPath: /workflows/theiaeuk/wf_theiaeuk_ont.wdl
+   testParameterFiles:
+    - /tests/inputs/empty.json
  - name: Cauris_CladeTyper_PHB
    subclass: WDL
    primaryDescriptorPath: /workflows/theiaeuk/wf_cauris_cladetyper.wdl
diff --git a/workflows/theiaeuk/wf_theiaeuk_ont.wdl b/workflows/theiaeuk/wf_theiaeuk_ont.wdl
new file mode 100644
index 000000000..2d9118962
--- /dev/null
+++ b/workflows/theiaeuk/wf_theiaeuk_ont.wdl
@@ -0,0 +1,108 @@
+version 1.0
+
+import "../utilities/wf_read_QC_trim_ont.wdl" as read_qc
+import "../../tasks/assembly/task_dragonflye.wdl" as dragonflye
+import "../../tasks/taxon_id/task_gambit.wdl" as gambit
+import "../utilities/wf_merlin_magic.wdl" as merlin_magic_workflow
+
+workflow theiaeuk_ont {
+  input {
+    File read1
+    String samplename
+    Int genome_length = 50000000 
+    String workflow_series = "theiaeuk"
+    String? assembler
+    String? assembler_options
+    Int dragonflye_cpu = 8
+    Int dragonflye_memory = 32
+    Int dragonflye_disk_size = 100
+    String medaka_model = "r941_min_hac_g507"
+    File gambit_db_genomes = "gs://theiagen-public-files-rp/terra/theiaeuk-files/gambit/221130-theiagen-fungal-v0.2.db"
+    File gambit_db_signatures = "gs://theiagen-public-files-rp/terra/theiaeuk-files/gambit/221130-theiagen-fungal-v0.2.h5"
+    Boolean assembly_only = true 
+    Boolean ont_data = true
+  }
+
+  call read_qc.read_QC_trim_ont as read_qc {
+    input:
+      read1 = read1,
+      samplename = samplename,
+      genome_length = genome_length,
+      workflow_series = workflow_series
+  }
+
+  call dragonflye.dragonflye {
+    input:
+      read1 = read_qc.read1_clean,
+      samplename = samplename,
+      assembler = assembler,
+      assembler_options = assembler_options,
+      genome_length = "${genome_length}",
+      medaka_model = medaka_model,
+      cpu = dragonflye_cpu,
+      memory = dragonflye_memory,
+      disk_size = dragonflye_disk_size
+  }
+
+  call gambit.gambit {
+    input:
+      assembly = dragonflye.assembly_fasta,
+      samplename = samplename,
+      gambit_db_genomes = gambit_db_genomes,
+      gambit_db_signatures = gambit_db_signatures
+  }
+
+   call merlin_magic_workflow.merlin_magic {
+    input:
+      samplename = samplename,
+      merlin_tag = gambit.merlin_tag,
+      assembly = dragonflye.assembly_fasta,
+      read1 = read_qc.read1_clean,
+      assembly_only = assembly_only,
+      ont_data = ont_data,
+      theiaeuk = true
+  }
+
+  output {
+    # Read QC outputs
+    File read1_clean = read_qc.read1_clean
+    String? nanoq_version = read_qc.nanoq_version
+    Int est_genome_length = read_qc.est_genome_length
+    # Assembly outputs
+    File assembly_fasta = dragonflye.assembly_fasta
+    File contigs_gfa = dragonflye.contigs_gfa
+    String dragonflye_version = dragonflye.dragonflye_version
+    # Gambit outputs
+    File gambit_report_file = gambit.gambit_report_file
+    File gambit_closest_genomes_file = gambit.gambit_closest_genomes_file
+    String gambit_predicted_taxon = gambit.gambit_predicted_taxon
+    String gambit_predicted_taxon_rank = gambit.gambit_predicted_taxon_rank
+    String gambit_next_taxon = gambit.gambit_next_taxon
+    String gambit_next_taxon_rank = gambit.gambit_next_taxon_rank
+    String gambit_version = gambit.gambit_version
+    String gambit_db_version = gambit.gambit_db_version
+    String merlin_tag = gambit.merlin_tag
+    String gambit_docker = gambit.gambit_docker
+    # C. auris specific outputs
+    String? clade_type = merlin_magic.clade_type
+    String? cladetyper_analysis_date = merlin_magic.cladetyper_analysis_date
+    String? cladetyper_version = merlin_magic.cladetyper_version
+    String? cladetyper_docker_image = merlin_magic.cladetyper_docker_image
+    String? cladetype_annotated_ref = merlin_magic.cladetype_annotated_ref
+    # Snippy variants outputs
+    String? snippy_variants_version = merlin_magic.snippy_variants_version
+    String? snippy_variants_query = merlin_magic.snippy_variants_query
+    String? snippy_variants_query_check = merlin_magic.snippy_variants_query_check
+    String? snippy_variants_hits = merlin_magic.snippy_variants_hits
+    String? snippy_variants_gene_query_results = merlin_magic.snippy_variants_gene_query_results
+    String? snippy_variants_outdir_tarball = merlin_magic.snippy_variants_outdir_tarball
+    String? snippy_variants_results = merlin_magic.snippy_variants_results
+    String? snippy_variants_bam = merlin_magic.snippy_variants_bam
+    String? snippy_variants_bai = merlin_magic.snippy_variants_bai
+    String? snippy_variants_summary = merlin_magic.snippy_variants_summary
+    String? snippy_variants_num_reads_aligned = merlin_magic.snippy_variants_num_reads_aligned
+    String? snippy_variants_coverage_tsv = merlin_magic.snippy_variants_coverage_tsv
+    String? snippy_variants_num_variants = merlin_magic.snippy_variants_num_variants
+    String? snippy_variants_percent_ref_coverage = merlin_magic.snippy_variants_percent_ref_coverage
+  }
+}
\ No newline at end of file
diff --git a/workflows/utilities/wf_merlin_magic.wdl b/workflows/utilities/wf_merlin_magic.wdl
index 690086a60..c59aa16c2 100644
--- a/workflows/utilities/wf_merlin_magic.wdl
+++ b/workflows/utilities/wf_merlin_magic.wdl
@@ -612,7 +612,7 @@ workflow merlin_magic {
           docker = cauris_cladetyper_docker_image
       }
       if (!assembly_only && !ont_data) {
-        call snippy.snippy_variants as snippy_cauris { # no ONT support right now
+        call snippy.snippy_variants as snippy_cauris {
           input:
             reference_genome_file = cladetyper.clade_spec_ref,
             read1 = select_first([read1]),
@@ -635,6 +635,30 @@ workflow merlin_magic {
             docker = snippy_gene_query_docker_image
         }
       }
+    
+      if (assembly_only && ont_data) {
+        call snippy.snippy_variants as snippy_cauris_ont {
+          input:
+            reference_genome_file = cladetyper.clade_spec_ref,
+            assembly_fasta = assembly,
+            samplename = samplename,
+            map_qual = snippy_map_qual,
+            base_quality = snippy_base_quality,
+            min_coverage = snippy_min_coverage,
+            min_frac = snippy_min_frac,
+            min_quality = snippy_min_quality,
+            maxsoft = snippy_maxsoft,
+            docker = snippy_variants_docker_image
+        }
+        call snippy_gene_query.snippy_gene_query as snippy_gene_query_cauris_ont {
+          input:
+            samplename = samplename,
+            snippy_variants_results = snippy_cauris_ont.snippy_variants_results,
+            reference = cladetyper.clade_spec_ref,
+            query_gene = select_first([snippy_query_gene, "FKS1,ERG11,FUR1"]),
+            docker = snippy_gene_query_docker_image
+        }
+      }
     }
     # Removing C.albicans subworkflow for now as current workflows not designed for diploid assembly
     # if (merlin_tag == "Candida albicans") {
@@ -963,20 +987,20 @@ workflow merlin_magic {
     String? cladetyper_docker_image = cladetyper.gambit_cladetyper_docker_image
     String? cladetype_annotated_ref = cladetyper.clade_spec_ref
     # snippy variants
-    String snippy_variants_reference_genome = select_first([snippy_cauris.snippy_variants_reference_genome, snippy_afumigatus.snippy_variants_reference_genome, snippy_crypto.snippy_variants_reference_genome, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_version = select_first([snippy_cauris.snippy_variants_version, snippy_afumigatus.snippy_variants_version, snippy_crypto.snippy_variants_version, "No matching taxon detected"])
-    String snippy_variants_query = select_first([snippy_gene_query_cauris.snippy_variants_query, snippy_gene_query_afumigatus.snippy_variants_query, snippy_gene_query_crypto.snippy_variants_query, "No matching taxon detected"])
-    String snippy_variants_query_check = select_first([snippy_gene_query_cauris.snippy_variants_query_check, snippy_gene_query_afumigatus.snippy_variants_query_check, snippy_gene_query_crypto.snippy_variants_query_check, "No matching taxon detected"])
-    String snippy_variants_hits = select_first([snippy_gene_query_cauris.snippy_variants_hits, snippy_gene_query_afumigatus.snippy_variants_hits, snippy_gene_query_crypto.snippy_variants_hits, "No matching taxon detected"])
-    String snippy_variants_gene_query_results = select_first([snippy_gene_query_cauris.snippy_variants_gene_query_results, snippy_gene_query_afumigatus.snippy_variants_gene_query_results, snippy_gene_query_crypto.snippy_variants_gene_query_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_outdir_tarball = select_first([snippy_cauris.snippy_variants_outdir_tarball, snippy_afumigatus.snippy_variants_outdir_tarball, snippy_crypto.snippy_variants_outdir_tarball, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_results = select_first([snippy_cauris.snippy_variants_results, snippy_afumigatus.snippy_variants_results, snippy_crypto.snippy_variants_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_bam = select_first([snippy_cauris.snippy_variants_bam, snippy_afumigatus.snippy_variants_bam, snippy_crypto.snippy_variants_bam, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_bai = select_first([snippy_cauris.snippy_variants_bai, snippy_afumigatus.snippy_variants_bai, snippy_crypto.snippy_variants_bai, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_summary = select_first([snippy_cauris.snippy_variants_summary, snippy_afumigatus.snippy_variants_summary, snippy_crypto.snippy_variants_summary, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_num_reads_aligned = select_first([snippy_cauris.snippy_variants_num_reads_aligned, snippy_afumigatus.snippy_variants_num_reads_aligned, snippy_crypto.snippy_variants_num_reads_aligned, "No matching taxon detected"])
-    String snippy_variants_coverage_tsv = select_first([snippy_cauris.snippy_variants_coverage_tsv, snippy_afumigatus.snippy_variants_coverage_tsv, snippy_crypto.snippy_variants_coverage_tsv, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_num_variants = select_first([snippy_cauris.snippy_variants_num_variants, snippy_afumigatus.snippy_variants_num_variants, snippy_crypto.snippy_variants_num_reads_aligned, "No matching taxon detected"])
-    String snippy_variants_percent_ref_coverage = select_first([snippy_cauris.snippy_variants_percent_ref_coverage, snippy_afumigatus.snippy_variants_percent_ref_coverage, snippy_crypto.snippy_variants_percent_ref_coverage, "No matching taxon detected"])
+    String snippy_variants_reference_genome = select_first([snippy_cauris.snippy_variants_reference_genome, snippy_cauris_ont.snippy_variants_reference_genome, snippy_afumigatus.snippy_variants_reference_genome, snippy_crypto.snippy_variants_reference_genome, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_version = select_first([snippy_cauris.snippy_variants_version, snippy_cauris_ont.snippy_variants_version,snippy_afumigatus.snippy_variants_version, snippy_crypto.snippy_variants_version, "No matching taxon detected"])
+    String snippy_variants_query = select_first([snippy_gene_query_cauris.snippy_variants_query, snippy_gene_query_cauris_ont.snippy_variants_query, snippy_gene_query_afumigatus.snippy_variants_query, snippy_gene_query_crypto.snippy_variants_query, "No matching taxon detected"])
+    String snippy_variants_query_check = select_first([snippy_gene_query_cauris.snippy_variants_query_check, snippy_gene_query_cauris_ont.snippy_variants_query_check, snippy_gene_query_afumigatus.snippy_variants_query_check, snippy_gene_query_crypto.snippy_variants_query_check, "No matching taxon detected"])
+    String snippy_variants_hits = select_first([snippy_gene_query_cauris.snippy_variants_hits, snippy_gene_query_cauris_ont.snippy_variants_hits, snippy_gene_query_afumigatus.snippy_variants_hits, snippy_gene_query_crypto.snippy_variants_hits, "No matching taxon detected"])
+    String snippy_variants_gene_query_results = select_first([snippy_gene_query_cauris.snippy_variants_gene_query_results, snippy_gene_query_cauris_ont.snippy_variants_gene_query_results, snippy_gene_query_afumigatus.snippy_variants_gene_query_results, snippy_gene_query_crypto.snippy_variants_gene_query_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_outdir_tarball = select_first([snippy_cauris.snippy_variants_outdir_tarball, snippy_cauris_ont.snippy_variants_outdir_tarball, snippy_afumigatus.snippy_variants_outdir_tarball, snippy_crypto.snippy_variants_outdir_tarball, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_results = select_first([snippy_cauris.snippy_variants_results, snippy_cauris_ont.snippy_variants_results,snippy_afumigatus.snippy_variants_results, snippy_crypto.snippy_variants_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_bam = select_first([snippy_cauris.snippy_variants_bam, snippy_cauris_ont.snippy_variants_bam, snippy_afumigatus.snippy_variants_bam, snippy_crypto.snippy_variants_bam, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_bai = select_first([snippy_cauris.snippy_variants_bai, snippy_cauris_ont.snippy_variants_bai, snippy_afumigatus.snippy_variants_bai, snippy_crypto.snippy_variants_bai, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_summary = select_first([snippy_cauris.snippy_variants_summary, snippy_cauris_ont.snippy_variants_summary, snippy_afumigatus.snippy_variants_summary, snippy_crypto.snippy_variants_summary, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_num_reads_aligned = select_first([snippy_cauris.snippy_variants_num_reads_aligned, snippy_cauris_ont.snippy_variants_num_reads_aligned, snippy_afumigatus.snippy_variants_num_reads_aligned, snippy_crypto.snippy_variants_num_reads_aligned, "No matching taxon detected"])
+    String snippy_variants_coverage_tsv = select_first([snippy_cauris.snippy_variants_coverage_tsv, snippy_cauris_ont.snippy_variants_coverage_tsv, snippy_afumigatus.snippy_variants_coverage_tsv, snippy_crypto.snippy_variants_coverage_tsv, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_num_variants = select_first([snippy_cauris.snippy_variants_num_variants, snippy_cauris_ont.snippy_variants_num_variants, snippy_afumigatus.snippy_variants_num_variants, snippy_crypto.snippy_variants_num_reads_aligned, "No matching taxon detected"])
+    String snippy_variants_percent_ref_coverage = select_first([snippy_cauris.snippy_variants_percent_ref_coverage, snippy_cauris_ont.snippy_variants_percent_ref_coverage, snippy_afumigatus.snippy_variants_percent_ref_coverage, snippy_crypto.snippy_variants_percent_ref_coverage, "No matching taxon detected"])
   }
 }
\ No newline at end of file

From 821b9903e439e27696c3df04789c0ea408f4632a Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Mon, 7 Oct 2024 17:05:35 +0000
Subject: [PATCH 02/13] Add specifics for description of cladetyper

---
 workflows/theiaeuk/wf_theiaeuk_ont.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/theiaeuk/wf_theiaeuk_ont.wdl b/workflows/theiaeuk/wf_theiaeuk_ont.wdl
index 2d9118962..4d2079c28 100644
--- a/workflows/theiaeuk/wf_theiaeuk_ont.wdl
+++ b/workflows/theiaeuk/wf_theiaeuk_ont.wdl
@@ -83,7 +83,7 @@ workflow theiaeuk_ont {
     String gambit_db_version = gambit.gambit_db_version
     String merlin_tag = gambit.merlin_tag
     String gambit_docker = gambit.gambit_docker
-    # C. auris specific outputs
+    # C. auris specific outputs for cladetyper
     String? clade_type = merlin_magic.clade_type
     String? cladetyper_analysis_date = merlin_magic.cladetyper_analysis_date
     String? cladetyper_version = merlin_magic.cladetyper_version

From 0dbc7581df8d555c1a8f07ff22950a9afc4e4f23 Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Mon, 7 Oct 2024 17:36:51 +0000
Subject: [PATCH 03/13] Added theiaeuk specific workflow_series logic to qc
 trim ont

---
 workflows/utilities/wf_read_QC_trim_ont.wdl | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/workflows/utilities/wf_read_QC_trim_ont.wdl b/workflows/utilities/wf_read_QC_trim_ont.wdl
index c03141251..3a5ac6058 100644
--- a/workflows/utilities/wf_read_QC_trim_ont.wdl
+++ b/workflows/utilities/wf_read_QC_trim_ont.wdl
@@ -121,6 +121,24 @@ workflow read_QC_trim_ont {
         samplename = samplename
     }
   }
+
+  if (workflow_series == "theiaeuk") {
+    # rasusa for random downsampling
+    call rasusa_task.rasusa as theiaeuk_rasusa {
+      input:
+        read1 = read1,
+        samplename = samplename,
+        coverage = downsampling_coverage,
+        genome_length = genome_length
+    }
+
+    # nanoq for filtering
+    call nanoq_task.nanoq as theiaeuk_nanoq {
+      input:
+        read1 = theiaeuk_rasusa.read1_subsampled,
+        samplename = samplename
+    }
+  }
   output { 
     # theiacov outputs
     # ncbi scrub outputs
@@ -144,7 +162,7 @@ workflow read_QC_trim_ont {
     Int est_genome_length = genome_length
 
     # nanoq outputs
-    File read1_clean = select_first([nanoq.filtered_read1, read_filtering.read1_clean])
+    File read1_clean = select_first([nanoq.filtered_read1, read_filtering.read1_clean, theiaeuk_nanoq.filtered_read1])
     String? nanoq_version = nanoq.version
 
     # rasusa outputs

From 63dcad3595f679bc6829243995bb850b349b6d11 Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Mon, 7 Oct 2024 19:39:22 +0000
Subject: [PATCH 04/13] Added versioning capture

---
 workflows/theiaeuk/wf_theiaeuk_ont.wdl | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/workflows/theiaeuk/wf_theiaeuk_ont.wdl b/workflows/theiaeuk/wf_theiaeuk_ont.wdl
index 4d2079c28..f59e6cd30 100644
--- a/workflows/theiaeuk/wf_theiaeuk_ont.wdl
+++ b/workflows/theiaeuk/wf_theiaeuk_ont.wdl
@@ -4,6 +4,7 @@ import "../utilities/wf_read_QC_trim_ont.wdl" as read_qc
 import "../../tasks/assembly/task_dragonflye.wdl" as dragonflye
 import "../../tasks/taxon_id/task_gambit.wdl" as gambit
 import "../utilities/wf_merlin_magic.wdl" as merlin_magic_workflow
+import "../../tasks/task_versioning.wdl" as versioning
 
 workflow theiaeuk_ont {
   input {
@@ -37,7 +38,7 @@ workflow theiaeuk_ont {
       samplename = samplename,
       assembler = assembler,
       assembler_options = assembler_options,
-      genome_length = "${genome_length}",
+      genome_length = genome_length,
       medaka_model = medaka_model,
       cpu = dragonflye_cpu,
       memory = dragonflye_memory,
@@ -63,7 +64,14 @@ workflow theiaeuk_ont {
       theiaeuk = true
   }
 
+  call versioning.version_capture {
+    input:
+  }
+
   output {
+    # Version Capture
+    String theiaeuk_ont_version = version_capture.phb_version
+    String theiaeuk_ont_analysis_date = version_capture.date
     # Read QC outputs
     File read1_clean = read_qc.read1_clean
     String? nanoq_version = read_qc.nanoq_version

From 6a45737190e24b34af9a5af2302e7c8cc3617786 Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Tue, 8 Oct 2024 12:36:13 +0000
Subject: [PATCH 05/13] Reordered logic for rasusa and nanoq

---
 workflows/utilities/wf_read_QC_trim_ont.wdl | 73 +++++++++------------
 1 file changed, 30 insertions(+), 43 deletions(-)

diff --git a/workflows/utilities/wf_read_QC_trim_ont.wdl b/workflows/utilities/wf_read_QC_trim_ont.wdl
index 3a5ac6058..00bddc0ac 100644
--- a/workflows/utilities/wf_read_QC_trim_ont.wdl
+++ b/workflows/utilities/wf_read_QC_trim_ont.wdl
@@ -79,27 +79,8 @@ workflow read_QC_trim_ont {
         target_organism = target_organism
     } 
   }
-  if ("~{workflow_series}" == "theiaprok") {
-    if ((call_kraken) && defined(kraken_db)) {
-      call kraken2.kraken2_standalone as kraken2_se {
-        input:
-          samplename = samplename,
-          read1 = read1,
-          kraken2_db = select_first([kraken_db]),
-          disk_size = kraken_disk_size,
-          memory = kraken_memory,
-          cpu = kraken_cpu
-      }
-      call kraken2.kraken2_parse_classified as kraken2_recalculate_abundances {
-        input:
-          samplename = samplename,
-          kraken2_report = kraken2_se.kraken2_report,
-          kraken2_classified_report = kraken2_se.kraken2_classified_report
-      }
-    } if ((call_kraken) && ! defined(kraken_db)) {
-      String kraken_db_warning = "Kraken database not defined"
-    }
 
+  if ("~{workflow_series}" == "theiaprok" || "~{workflow_series}" == "theiaeuk") {
     # rasusa for random downsampling
     call rasusa_task.rasusa {
       input:
@@ -108,35 +89,41 @@ workflow read_QC_trim_ont {
         coverage = downsampling_coverage,
         genome_length = genome_length
     }
-    # tiptoft for plasmid detection
-    call tiptoft_task.tiptoft {
-      input:
-        read1 = read1,
-        samplename = samplename
-    }  
-    # nanoq/filtlong (default min length 500)
+
+    # nanoq for filtering
     call nanoq_task.nanoq {
       input:
         read1 = rasusa.read1_subsampled,
         samplename = samplename
     }
-  }
 
-  if (workflow_series == "theiaeuk") {
-    # rasusa for random downsampling
-    call rasusa_task.rasusa as theiaeuk_rasusa {
-      input:
-        read1 = read1,
-        samplename = samplename,
-        coverage = downsampling_coverage,
-        genome_length = genome_length
-    }
+    if ("~{workflow_series}" == "theiaprok") {
+      # tiptoft for plasmid detection
+      call tiptoft_task.tiptoft {
+        input:
+          read1 = read1,
+          samplename = samplename
+      }
 
-    # nanoq for filtering
-    call nanoq_task.nanoq as theiaeuk_nanoq {
-      input:
-        read1 = theiaeuk_rasusa.read1_subsampled,
-        samplename = samplename
+      if (call_kraken && defined(kraken_db)) {
+        call kraken2.kraken2_standalone as kraken2_se {
+          input:
+            samplename = samplename,
+            read1 = read1,
+            kraken2_db = select_first([kraken_db]),
+            disk_size = kraken_disk_size,
+            memory = kraken_memory,
+            cpu = kraken_cpu
+        }
+        call kraken2.kraken2_parse_classified as kraken2_recalculate_abundances {
+          input:
+            samplename = samplename,
+            kraken2_report = kraken2_se.kraken2_report,
+            kraken2_classified_report = kraken2_se.kraken2_classified_report
+        } 
+      } if ((call_kraken) && ! defined(kraken_db)) {
+          String kraken_db_warning = "Kraken database not defined"
+        }
     }
   }
   output { 
@@ -162,7 +149,7 @@ workflow read_QC_trim_ont {
     Int est_genome_length = genome_length
 
     # nanoq outputs
-    File read1_clean = select_first([nanoq.filtered_read1, read_filtering.read1_clean, theiaeuk_nanoq.filtered_read1])
+    File read1_clean = select_first([nanoq.filtered_read1, read_filtering.read1_clean])
     String? nanoq_version = nanoq.version
 
     # rasusa outputs

From af723142d3db67c4e838f95c31193a28b2346906 Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Tue, 8 Oct 2024 12:38:03 +0000
Subject: [PATCH 06/13] Removed options for merlin magic that should be hidden

---
 workflows/theiaeuk/wf_theiaeuk_ont.wdl | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/workflows/theiaeuk/wf_theiaeuk_ont.wdl b/workflows/theiaeuk/wf_theiaeuk_ont.wdl
index f59e6cd30..224473b88 100644
--- a/workflows/theiaeuk/wf_theiaeuk_ont.wdl
+++ b/workflows/theiaeuk/wf_theiaeuk_ont.wdl
@@ -20,8 +20,6 @@ workflow theiaeuk_ont {
     String medaka_model = "r941_min_hac_g507"
     File gambit_db_genomes = "gs://theiagen-public-files-rp/terra/theiaeuk-files/gambit/221130-theiagen-fungal-v0.2.db"
     File gambit_db_signatures = "gs://theiagen-public-files-rp/terra/theiaeuk-files/gambit/221130-theiagen-fungal-v0.2.h5"
-    Boolean assembly_only = true 
-    Boolean ont_data = true
   }
 
   call read_qc.read_QC_trim_ont as read_qc {
@@ -58,9 +56,8 @@ workflow theiaeuk_ont {
       samplename = samplename,
       merlin_tag = gambit.merlin_tag,
       assembly = dragonflye.assembly_fasta,
-      read1 = read_qc.read1_clean,
-      assembly_only = assembly_only,
-      ont_data = ont_data,
+      assembly_only = true,
+      ont_data = true,
       theiaeuk = true
   }
 

From 4bd515d79772424b9f3fc43e7e4e5e51134f7571 Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Tue, 8 Oct 2024 13:39:59 +0000
Subject: [PATCH 07/13] Reorder logic for snippy variant if tag is C.Auris

---
 workflows/utilities/wf_merlin_magic.wdl | 94 ++++++++++++-------------
 1 file changed, 45 insertions(+), 49 deletions(-)

diff --git a/workflows/utilities/wf_merlin_magic.wdl b/workflows/utilities/wf_merlin_magic.wdl
index c59aa16c2..f010353f3 100644
--- a/workflows/utilities/wf_merlin_magic.wdl
+++ b/workflows/utilities/wf_merlin_magic.wdl
@@ -612,54 +612,50 @@ workflow merlin_magic {
           docker = cauris_cladetyper_docker_image
       }
       if (!assembly_only && !ont_data) {
-        call snippy.snippy_variants as snippy_cauris {
-          input:
-            reference_genome_file = cladetyper.clade_spec_ref,
-            read1 = select_first([read1]),
-            read2 = read2,
-            samplename = samplename,
-            map_qual = snippy_map_qual,
-            base_quality = snippy_base_quality,
-            min_coverage = snippy_min_coverage,
-            min_frac = snippy_min_frac,
-            min_quality = snippy_min_quality,
-            maxsoft = snippy_maxsoft,
-            docker = snippy_variants_docker_image
-        }
-        call snippy_gene_query.snippy_gene_query as snippy_gene_query_cauris {
-          input:
-            samplename = samplename,
-            snippy_variants_results = snippy_cauris.snippy_variants_results,
-            reference = cladetyper.clade_spec_ref,
-            query_gene = select_first([snippy_query_gene, "FKS1,lanosterol.14-alpha.demethylase,uracil.phosphoribosyltransferase"]),
-            docker = snippy_gene_query_docker_image
-        }
+      call snippy.snippy_variants as snippy_cauris {
+        input:
+          reference_genome_file = cladetyper.clade_spec_ref,
+          read1 = select_first([read1]),
+          read2 = read2,
+          samplename = samplename,
+          map_qual = snippy_map_qual,
+          base_quality = snippy_base_quality,
+          min_coverage = snippy_min_coverage,
+          min_frac = snippy_min_frac,
+          min_quality = snippy_min_quality,
+          maxsoft = snippy_maxsoft,
+          docker = snippy_variants_docker_image
       }
-    
-      if (assembly_only && ont_data) {
-        call snippy.snippy_variants as snippy_cauris_ont {
-          input:
-            reference_genome_file = cladetyper.clade_spec_ref,
-            assembly_fasta = assembly,
-            samplename = samplename,
-            map_qual = snippy_map_qual,
-            base_quality = snippy_base_quality,
-            min_coverage = snippy_min_coverage,
-            min_frac = snippy_min_frac,
-            min_quality = snippy_min_quality,
-            maxsoft = snippy_maxsoft,
-            docker = snippy_variants_docker_image
-        }
-        call snippy_gene_query.snippy_gene_query as snippy_gene_query_cauris_ont {
-          input:
-            samplename = samplename,
-            snippy_variants_results = snippy_cauris_ont.snippy_variants_results,
-            reference = cladetyper.clade_spec_ref,
-            query_gene = select_first([snippy_query_gene, "FKS1,ERG11,FUR1"]),
-            docker = snippy_gene_query_docker_image
-        }
+    }
+
+    if (assembly_only && ont_data) {
+      call snippy.snippy_variants as snippy_cauris_ont {
+        input:
+          reference_genome_file = cladetyper.clade_spec_ref,
+          assembly_fasta = assembly,
+          samplename = samplename,
+          map_qual = snippy_map_qual,
+          base_quality = snippy_base_quality,
+          min_coverage = snippy_min_coverage,
+          min_frac = snippy_min_frac,
+          min_quality = snippy_min_quality,
+          maxsoft = snippy_maxsoft,
+          docker = snippy_variants_docker_image
       }
     }
+    call snippy_gene_query.snippy_gene_query as snippy_gene_query_cauris {
+      input:
+        samplename = samplename,
+        snippy_variants_results = select_first([snippy_cauris.snippy_variants_results, snippy_cauris_ont.snippy_variants_results]),
+        reference = cladetyper.clade_spec_ref,
+        query_gene = select_first([
+          snippy_query_gene,
+          if (assembly_only && ont_data) then "FKS1,ERG11,FUR1" 
+          else "FKS1,lanosterol.14-alpha.demethylase,uracil.phosphoribosyltransferase"
+        ]),
+        docker = snippy_gene_query_docker_image
+    }
+  }
     # Removing C.albicans subworkflow for now as current workflows not designed for diploid assembly
     # if (merlin_tag == "Candida albicans") {
     #   if (!assembly_only && !ont_data) {
@@ -989,10 +985,10 @@ workflow merlin_magic {
     # snippy variants
     String snippy_variants_reference_genome = select_first([snippy_cauris.snippy_variants_reference_genome, snippy_cauris_ont.snippy_variants_reference_genome, snippy_afumigatus.snippy_variants_reference_genome, snippy_crypto.snippy_variants_reference_genome, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
     String snippy_variants_version = select_first([snippy_cauris.snippy_variants_version, snippy_cauris_ont.snippy_variants_version,snippy_afumigatus.snippy_variants_version, snippy_crypto.snippy_variants_version, "No matching taxon detected"])
-    String snippy_variants_query = select_first([snippy_gene_query_cauris.snippy_variants_query, snippy_gene_query_cauris_ont.snippy_variants_query, snippy_gene_query_afumigatus.snippy_variants_query, snippy_gene_query_crypto.snippy_variants_query, "No matching taxon detected"])
-    String snippy_variants_query_check = select_first([snippy_gene_query_cauris.snippy_variants_query_check, snippy_gene_query_cauris_ont.snippy_variants_query_check, snippy_gene_query_afumigatus.snippy_variants_query_check, snippy_gene_query_crypto.snippy_variants_query_check, "No matching taxon detected"])
-    String snippy_variants_hits = select_first([snippy_gene_query_cauris.snippy_variants_hits, snippy_gene_query_cauris_ont.snippy_variants_hits, snippy_gene_query_afumigatus.snippy_variants_hits, snippy_gene_query_crypto.snippy_variants_hits, "No matching taxon detected"])
-    String snippy_variants_gene_query_results = select_first([snippy_gene_query_cauris.snippy_variants_gene_query_results, snippy_gene_query_cauris_ont.snippy_variants_gene_query_results, snippy_gene_query_afumigatus.snippy_variants_gene_query_results, snippy_gene_query_crypto.snippy_variants_gene_query_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_query = select_first([snippy_gene_query_cauris.snippy_variants_query, snippy_gene_query_afumigatus.snippy_variants_query, snippy_gene_query_crypto.snippy_variants_query, "No matching taxon detected"])
+    String snippy_variants_query_check = select_first([snippy_gene_query_cauris.snippy_variants_query_check, snippy_gene_query_afumigatus.snippy_variants_query_check, snippy_gene_query_crypto.snippy_variants_query_check, "No matching taxon detected"])
+    String snippy_variants_hits = select_first([snippy_gene_query_cauris.snippy_variants_hits, snippy_gene_query_afumigatus.snippy_variants_hits, snippy_gene_query_crypto.snippy_variants_hits, "No matching taxon detected"])
+    String snippy_variants_gene_query_results = select_first([snippy_gene_query_cauris.snippy_variants_gene_query_results, snippy_gene_query_afumigatus.snippy_variants_gene_query_results, snippy_gene_query_crypto.snippy_variants_gene_query_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
     String snippy_variants_outdir_tarball = select_first([snippy_cauris.snippy_variants_outdir_tarball, snippy_cauris_ont.snippy_variants_outdir_tarball, snippy_afumigatus.snippy_variants_outdir_tarball, snippy_crypto.snippy_variants_outdir_tarball, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
     String snippy_variants_results = select_first([snippy_cauris.snippy_variants_results, snippy_cauris_ont.snippy_variants_results,snippy_afumigatus.snippy_variants_results, snippy_crypto.snippy_variants_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
     String snippy_variants_bam = select_first([snippy_cauris.snippy_variants_bam, snippy_cauris_ont.snippy_variants_bam, snippy_afumigatus.snippy_variants_bam, snippy_crypto.snippy_variants_bam, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])

From 08a92fb73f27de2a6f6dc53c9a4a446098f2ca1b Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Tue, 8 Oct 2024 13:57:39 +0000
Subject: [PATCH 08/13] Added read qc and assembly qc

---
 workflows/theiaeuk/wf_theiaeuk_ont.wdl | 78 ++++++++++++++++++++++++--
 1 file changed, 74 insertions(+), 4 deletions(-)

diff --git a/workflows/theiaeuk/wf_theiaeuk_ont.wdl b/workflows/theiaeuk/wf_theiaeuk_ont.wdl
index 224473b88..a4a721084 100644
--- a/workflows/theiaeuk/wf_theiaeuk_ont.wdl
+++ b/workflows/theiaeuk/wf_theiaeuk_ont.wdl
@@ -5,6 +5,9 @@ import "../../tasks/assembly/task_dragonflye.wdl" as dragonflye
 import "../../tasks/taxon_id/task_gambit.wdl" as gambit
 import "../utilities/wf_merlin_magic.wdl" as merlin_magic_workflow
 import "../../tasks/task_versioning.wdl" as versioning
+import "../../tasks/quality_control/basic_statistics/task_nanoplot.wdl" as nanoplot_task
+import "../../tasks/quality_control/basic_statistics/task_quast.wdl" as quast_task
+import "../../tasks/quality_control/advanced_metrics/task_busco.wdl" as busco_task
 
 workflow theiaeuk_ont {
   input {
@@ -22,6 +25,10 @@ workflow theiaeuk_ont {
     File gambit_db_signatures = "gs://theiagen-public-files-rp/terra/theiaeuk-files/gambit/221130-theiagen-fungal-v0.2.h5"
   }
 
+  call versioning.version_capture {
+    input:
+  }
+
   call read_qc.read_QC_trim_ont as read_qc {
     input:
       read1 = read1,
@@ -42,6 +49,32 @@ workflow theiaeuk_ont {
       memory = dragonflye_memory,
       disk_size = dragonflye_disk_size
   }
+  #call quast on the assembly
+  call quast_task.quast {
+    input:
+      assembly = dragonflye.assembly_fasta,
+      samplename = samplename
+  }
+  # nanoplot for raw reads
+  call nanoplot_task.nanoplot as nanoplot_raw {
+    input:
+      read1 = read1,
+      samplename = samplename,
+      est_genome_length = select_first([genome_length, quast.genome_length])
+  }
+  # nanoplot for cleaned reads
+  call nanoplot_task.nanoplot as nanoplot_clean {
+    input:
+      read1 = read_qc.read1_clean,
+      samplename = samplename,
+      est_genome_length = select_first([genome_length, quast.genome_length])
+  }
+  # busco on the assembly
+  call busco_task.busco {
+    input:
+      assembly = dragonflye.assembly_fasta,
+      samplename = samplename
+  }
 
   call gambit.gambit {
     input:
@@ -61,10 +94,6 @@ workflow theiaeuk_ont {
       theiaeuk = true
   }
 
-  call versioning.version_capture {
-    input:
-  }
-
   output {
     # Version Capture
     String theiaeuk_ont_version = version_capture.phb_version
@@ -77,6 +106,47 @@ workflow theiaeuk_ont {
     File assembly_fasta = dragonflye.assembly_fasta
     File contigs_gfa = dragonflye.contigs_gfa
     String dragonflye_version = dragonflye.dragonflye_version
+    # Read QC - nanoplot raw outputs
+    File? nanoplot_html_raw = nanoplot_raw.nanoplot_html
+    File? nanoplot_tsv_raw = nanoplot_raw.nanoplot_tsv
+    Int? nanoplot_num_reads_raw1 = nanoplot_raw.num_reads
+    Float? nanoplot_r1_median_readlength_raw = nanoplot_raw.median_readlength
+    Float? nanoplot_r1_mean_readlength_raw = nanoplot_raw.mean_readlength
+    Float? nanoplot_r1_stdev_readlength_raw = nanoplot_raw.stdev_readlength
+    Float? nanoplot_r1_n50_raw = nanoplot_raw.n50
+    Float? nanoplot_r1_mean_q_raw = nanoplot_raw.mean_q
+    Float? nanoplot_r1_median_q_raw = nanoplot_raw.median_q
+    Float? nanoplot_r1_est_coverage_raw = nanoplot_raw.est_coverage
+    # Read QC - nanoplot clean outputs
+    File? nanoplot_html_clean = nanoplot_clean.nanoplot_html
+    File? nanoplot_tsv_clean = nanoplot_clean.nanoplot_tsv
+    Int? nanoplot_num_reads_clean1 = nanoplot_clean.num_reads
+    Float? nanoplot_r1_median_readlength_clean = nanoplot_clean.median_readlength
+    Float? nanoplot_r1_mean_readlength_clean = nanoplot_clean.mean_readlength
+    Float? nanoplot_r1_stdev_readlength_clean = nanoplot_clean.stdev_readlength
+    Float? nanoplot_r1_n50_clean = nanoplot_clean.n50
+    Float? nanoplot_r1_mean_q_clean = nanoplot_clean.mean_q
+    Float? nanoplot_r1_median_q_clean = nanoplot_clean.median_q
+    Float? nanoplot_r1_est_coverage_clean = nanoplot_clean.est_coverage
+    # Read QC - nanoplot general outputs
+    String? nanoplot_version = nanoplot_raw.nanoplot_version
+    String? nanoplot_docker = nanoplot_raw.nanoplot_docker
+    # Assembly QC - quast outputs
+    File? quast_report = quast.quast_report
+    String? quast_version = quast.version
+    Int? assembly_length = quast.genome_length
+    Int? number_contigs = quast.number_contigs
+    Int? n50_value = quast.n50_value
+    Float? quast_gc_percent = quast.gc_percent
+    # Assembly QC - nanoplot outputs
+    Float? est_coverage_raw = nanoplot_raw.est_coverage
+    Float? est_coverage_clean = nanoplot_clean.est_coverage
+    # Assembly QC - busco outputs
+    String? busco_version = busco.busco_version
+    String? busco_docker = busco.busco_docker
+    String? busco_database = busco.busco_database
+    String? busco_results = busco.busco_results
+    File? busco_report = busco.busco_report
     # Gambit outputs
     File gambit_report_file = gambit.gambit_report_file
     File gambit_closest_genomes_file = gambit.gambit_closest_genomes_file

From 5cc94078de1b7d7ad4a0cae8da610eb43a198e94 Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Tue, 8 Oct 2024 16:56:24 +0000
Subject: [PATCH 09/13] updated md5 sum

---
 tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml | 2 +-
 tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
index d2cedb29b..bae74e2e5 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -633,7 +633,7 @@
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
       md5sum: 6d9dd969e2144ca23f2a0e101e6b6966
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
-      md5sum: 8ab95440118d06dd3c07765a19e876e7
+      md5sum: ba96a542bb0896569fee6136f712fdd1
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_pe.wdl
       contains: ["version", "QC", "output"]
     - path: miniwdl_run/workflow.log
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
index d19f1319e..3a891aaa8 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -526,7 +526,7 @@
     - path: miniwdl_run/wdl/tasks/gene_typing/drug_resistance/task_resfinder.wdl
       md5sum: 27528633723303b462d095b642649453
     - path: miniwdl_run/wdl/tasks/gene_typing/variant_detection/task_snippy_variants.wdl
-      md5sum: 284ce680b52e7e1c1753537b344fa161
+      md5sum: 3b9e04569d7e856dcc649b7726b306b7
     - path: miniwdl_run/wdl/tasks/quality_control/read_filtering/task_bbduk.wdl
       md5sum: aec6ef024d6dff31723f44290f6b9cf5
     - path: miniwdl_run/wdl/tasks/quality_control/advanced_metrics/task_busco.wdl
@@ -596,7 +596,7 @@
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
       md5sum: 5aa25e4fad466f92c96a7c138aca0d20
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
-      md5sum: 8ab95440118d06dd3c07765a19e876e7
+      md5sum: ba96a542bb0896569fee6136f712fdd1
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl
       md5sum: d11bfe33fdd96eab28892be5a01c1c7d
     - path: miniwdl_run/workflow.log

From 021dbb71640af8179eed7bc22b02857e0b7e7c98 Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Tue, 8 Oct 2024 18:21:54 +0000
Subject: [PATCH 10/13] Initial commits for theiaeuk CI

---
 tests/config/pytest_filter.yml                | 10 +++++++++
 tests/inputs/theiaeuk/wf_theiaeuk_ont.json    | 17 ++++++++++++++
 .../theiaeuk/wf_theiaeuk_ont_cromwell.json    |  7 ++++++
 .../theiaeuk/test_wf_theiaeuk_ont.yml         | 22 +++++++++++++++++++
 4 files changed, 56 insertions(+)
 create mode 100644 tests/inputs/theiaeuk/wf_theiaeuk_ont.json
 create mode 100644 tests/inputs/theiaeuk/wf_theiaeuk_ont_cromwell.json
 create mode 100644 tests/workflows/theiaeuk/test_wf_theiaeuk_ont.yml

diff --git a/tests/config/pytest_filter.yml b/tests/config/pytest_filter.yml
index 5effea33a..838c21d33 100644
--- a/tests/config/pytest_filter.yml
+++ b/tests/config/pytest_filter.yml
@@ -171,3 +171,13 @@ wf_theiaprok_illumina_se:
   - tasks/species_typing/multi/task_ts_mlst.wdl
   - tasks/taxon_id/contamination/task_kraken2.wdl
   - tasks/taxon_id/contamination/task_midas.wdl
+
+# wf_theiaeuk_ont:
+#   - workflows/theiaeuk/wf_theiaeuk_ont.wdl
+#   - tasks/assembly/task_dragonflye.wdl
+#   - tasks/taxon_id/task_gambit.wdl
+#   - workflows/utilities/wf_merlin_magic.wdl
+#   - tasks/quality_control/basic_statistics/task_nanoplot.wdl
+#   - tasks/quality_control/basic_statistics/task_quast.wdl
+#   - tasks/quality_control/advanced_metrics/task_busco.wdl
+#   - tasks/task_versioning.wdl
\ No newline at end of file
diff --git a/tests/inputs/theiaeuk/wf_theiaeuk_ont.json b/tests/inputs/theiaeuk/wf_theiaeuk_ont.json
new file mode 100644
index 000000000..e027c6387
--- /dev/null
+++ b/tests/inputs/theiaeuk/wf_theiaeuk_ont.json
@@ -0,0 +1,17 @@
+{
+    "theiaeuk_ont.samplename": "test",
+    "theiaeuk_ont.read1": "tests/data/theiacov/fastqs/ont/ont.fastq.gz",
+    "theiaeuk_ont.dragonflye.assembler": "flye",
+    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade1": "./tests/inputs/empty-for-test.txt",
+    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade1_annotated": "./tests/inputs/empty-for-test.txt",
+    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade2": "./tests/inputs/empty-for-test.txt",
+    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade2_annotated": "./tests/inputs/empty-for-test.txt",
+    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade3": "./tests/inputs/empty-for-test.txt",
+    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade3_annotated": "./tests/inputs/empty-for-test.txt",
+    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade4": "./tests/inputs/empty-for-test.txt",
+    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade4_annotated": "./tests/inputs/empty-for-test.txt",
+    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade5": "./tests/inputs/empty-for-test.txt",
+    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade5_annotated": "./tests/inputs/empty-for-test.txt",
+    "theiaeuk_ont.gambit.gambit_db_signatures": "./tests/inputs/completely-empty-for-test.txt",
+    "theiaeuk_ont.gambit.gambit_db_genomes": "./tests/inputs/completely-empty-for-test.txt"
+}
\ No newline at end of file
diff --git a/tests/inputs/theiaeuk/wf_theiaeuk_ont_cromwell.json b/tests/inputs/theiaeuk/wf_theiaeuk_ont_cromwell.json
new file mode 100644
index 000000000..0f9c135b5
--- /dev/null
+++ b/tests/inputs/theiaeuk/wf_theiaeuk_ont_cromwell.json
@@ -0,0 +1,7 @@
+{
+    "theiaeuk_ont.samplename": "test",
+    "theiaeuk_ont.read1": "tests/data/theiacov/fastqs/ont/ont.fastq.gz",
+    "theiaeuk_ont.dragonflye.assembler": "flye",
+    "theiaeuk_ont.gambit.gambit_db_signatures": "./tests/inputs/completely-empty-for-test.txt",
+    "theiaeuk_ont.gambit.gambit_db_genomes": "./tests/inputs/completely-empty-for-test.txt"
+}
\ No newline at end of file
diff --git a/tests/workflows/theiaeuk/test_wf_theiaeuk_ont.yml b/tests/workflows/theiaeuk/test_wf_theiaeuk_ont.yml
new file mode 100644
index 000000000..e070eed9d
--- /dev/null
+++ b/tests/workflows/theiaeuk/test_wf_theiaeuk_ont.yml
@@ -0,0 +1,22 @@
+- name: theiaeuk_ont_cromwell
+  command: cromwell run -i ./tests/inputs/theiaeuk/wf_theiaeuk_ont_cromwell.json -m metadata.json ./workflows/theiaeuk/wf_theiaeuk_ont.wdl
+  tags:
+    - wf_theiaeuk_ont
+    - wf_theiaeuk_ont_cromwell
+  files:
+    - path: log.err
+    - path: log.out
+      contains: ["workflow finished with status 'Succeeded'", "theiaeuk_ont", "Done"]
+    - path: metadata.json
+      contains: ["outputs", "theiaeuk_ont", "Succeeded"]
+
+- name: theiaeuk_ont_miniwdl
+  command: miniwdl run -i ./tests/inputs/theiaeuk/wf_theiaeuk_ont.json -d miniwdl_run/. --verbose --error-json ./workflows/theiaeuk/wf_theiaeuk_ont.wdl
+  tags:
+    - wf_theiaeuk_ont
+    - wf_theiaeuk_ont_miniwdl
+  files:
+    - path: miniwdl_run/call-someTask/command
+      md5sum: expectedMd5sumHere
+    - path: miniwdl_run/call-someTask/inputs.json
+      contains: ["expectedContent", "moreExpectedContent"]
\ No newline at end of file

From 767f33a57039a7455ec5626958432d11bb81bef0 Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Wed, 9 Oct 2024 18:39:25 +0000
Subject: [PATCH 11/13] Removed unecessary tests

---
 tests/config/pytest_filter.yml                | 12 +---------
 tests/inputs/theiaeuk/wf_theiaeuk_ont.json    | 17 --------------
 .../theiaeuk/wf_theiaeuk_ont_cromwell.json    |  7 ------
 .../theiaeuk/test_wf_theiaeuk_ont.yml         | 22 -------------------
 4 files changed, 1 insertion(+), 57 deletions(-)
 delete mode 100644 tests/inputs/theiaeuk/wf_theiaeuk_ont.json
 delete mode 100644 tests/inputs/theiaeuk/wf_theiaeuk_ont_cromwell.json
 delete mode 100644 tests/workflows/theiaeuk/test_wf_theiaeuk_ont.yml

diff --git a/tests/config/pytest_filter.yml b/tests/config/pytest_filter.yml
index 838c21d33..b98a79f7b 100644
--- a/tests/config/pytest_filter.yml
+++ b/tests/config/pytest_filter.yml
@@ -170,14 +170,4 @@ wf_theiaprok_illumina_se:
   - tasks/species_typing/mycobacterium/task_tbprofiler.wdl
   - tasks/species_typing/multi/task_ts_mlst.wdl
   - tasks/taxon_id/contamination/task_kraken2.wdl
-  - tasks/taxon_id/contamination/task_midas.wdl
-
-# wf_theiaeuk_ont:
-#   - workflows/theiaeuk/wf_theiaeuk_ont.wdl
-#   - tasks/assembly/task_dragonflye.wdl
-#   - tasks/taxon_id/task_gambit.wdl
-#   - workflows/utilities/wf_merlin_magic.wdl
-#   - tasks/quality_control/basic_statistics/task_nanoplot.wdl
-#   - tasks/quality_control/basic_statistics/task_quast.wdl
-#   - tasks/quality_control/advanced_metrics/task_busco.wdl
-#   - tasks/task_versioning.wdl
\ No newline at end of file
+  - tasks/taxon_id/contamination/task_midas.wdl
\ No newline at end of file
diff --git a/tests/inputs/theiaeuk/wf_theiaeuk_ont.json b/tests/inputs/theiaeuk/wf_theiaeuk_ont.json
deleted file mode 100644
index e027c6387..000000000
--- a/tests/inputs/theiaeuk/wf_theiaeuk_ont.json
+++ /dev/null
@@ -1,17 +0,0 @@
-{
-    "theiaeuk_ont.samplename": "test",
-    "theiaeuk_ont.read1": "tests/data/theiacov/fastqs/ont/ont.fastq.gz",
-    "theiaeuk_ont.dragonflye.assembler": "flye",
-    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade1": "./tests/inputs/empty-for-test.txt",
-    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade1_annotated": "./tests/inputs/empty-for-test.txt",
-    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade2": "./tests/inputs/empty-for-test.txt",
-    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade2_annotated": "./tests/inputs/empty-for-test.txt",
-    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade3": "./tests/inputs/empty-for-test.txt",
-    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade3_annotated": "./tests/inputs/empty-for-test.txt",
-    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade4": "./tests/inputs/empty-for-test.txt",
-    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade4_annotated": "./tests/inputs/empty-for-test.txt",
-    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade5": "./tests/inputs/empty-for-test.txt",
-    "theiaeuk_ont.merlin_magic.cladetyper_ref_clade5_annotated": "./tests/inputs/empty-for-test.txt",
-    "theiaeuk_ont.gambit.gambit_db_signatures": "./tests/inputs/completely-empty-for-test.txt",
-    "theiaeuk_ont.gambit.gambit_db_genomes": "./tests/inputs/completely-empty-for-test.txt"
-}
\ No newline at end of file
diff --git a/tests/inputs/theiaeuk/wf_theiaeuk_ont_cromwell.json b/tests/inputs/theiaeuk/wf_theiaeuk_ont_cromwell.json
deleted file mode 100644
index 0f9c135b5..000000000
--- a/tests/inputs/theiaeuk/wf_theiaeuk_ont_cromwell.json
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-    "theiaeuk_ont.samplename": "test",
-    "theiaeuk_ont.read1": "tests/data/theiacov/fastqs/ont/ont.fastq.gz",
-    "theiaeuk_ont.dragonflye.assembler": "flye",
-    "theiaeuk_ont.gambit.gambit_db_signatures": "./tests/inputs/completely-empty-for-test.txt",
-    "theiaeuk_ont.gambit.gambit_db_genomes": "./tests/inputs/completely-empty-for-test.txt"
-}
\ No newline at end of file
diff --git a/tests/workflows/theiaeuk/test_wf_theiaeuk_ont.yml b/tests/workflows/theiaeuk/test_wf_theiaeuk_ont.yml
deleted file mode 100644
index e070eed9d..000000000
--- a/tests/workflows/theiaeuk/test_wf_theiaeuk_ont.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-- name: theiaeuk_ont_cromwell
-  command: cromwell run -i ./tests/inputs/theiaeuk/wf_theiaeuk_ont_cromwell.json -m metadata.json ./workflows/theiaeuk/wf_theiaeuk_ont.wdl
-  tags:
-    - wf_theiaeuk_ont
-    - wf_theiaeuk_ont_cromwell
-  files:
-    - path: log.err
-    - path: log.out
-      contains: ["workflow finished with status 'Succeeded'", "theiaeuk_ont", "Done"]
-    - path: metadata.json
-      contains: ["outputs", "theiaeuk_ont", "Succeeded"]
-
-- name: theiaeuk_ont_miniwdl
-  command: miniwdl run -i ./tests/inputs/theiaeuk/wf_theiaeuk_ont.json -d miniwdl_run/. --verbose --error-json ./workflows/theiaeuk/wf_theiaeuk_ont.wdl
-  tags:
-    - wf_theiaeuk_ont
-    - wf_theiaeuk_ont_miniwdl
-  files:
-    - path: miniwdl_run/call-someTask/command
-      md5sum: expectedMd5sumHere
-    - path: miniwdl_run/call-someTask/inputs.json
-      contains: ["expectedContent", "moreExpectedContent"]
\ No newline at end of file

From d46d58f3839f8a89b181de7c7ab88ba8c17922bd Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Fri, 18 Oct 2024 18:23:16 +0000
Subject: [PATCH 12/13] Added ont support for A. fumigatus & C. neoformans

---
 workflows/utilities/wf_merlin_magic.wdl | 61 +++++++++++++++++++------
 1 file changed, 46 insertions(+), 15 deletions(-)

diff --git a/workflows/utilities/wf_merlin_magic.wdl b/workflows/utilities/wf_merlin_magic.wdl
index f010353f3..b02e978b1 100644
--- a/workflows/utilities/wf_merlin_magic.wdl
+++ b/workflows/utilities/wf_merlin_magic.wdl
@@ -697,16 +697,32 @@ workflow merlin_magic {
             maxsoft = snippy_maxsoft,
             docker = snippy_variants_docker_image
         }
+      }
+
+      if (assembly_only && ont_data) {
+        call snippy.snippy_variants as snippy_afumigatus_ont {
+          input:
+            reference_genome_file = snippy_reference_afumigatus,
+            assembly_fasta = assembly,
+            samplename = samplename,
+            map_qual = snippy_map_qual,
+            base_quality = snippy_base_quality,
+            min_coverage = snippy_min_coverage,
+            min_frac = snippy_min_frac,
+            min_quality = snippy_min_quality,
+            maxsoft = snippy_maxsoft,
+            docker = snippy_variants_docker_image
+        }
+      }
         call snippy_gene_query.snippy_gene_query as snippy_gene_query_afumigatus {
           input:
             samplename = samplename,
-            snippy_variants_results = snippy_afumigatus.snippy_variants_results,
+            snippy_variants_results = select_first([snippy_afumigatus.snippy_variants_results, snippy_afumigatus_ont.snippy_variants_results]),
             reference = snippy_reference_afumigatus,
             query_gene = select_first([snippy_query_gene, "Cyp51A,HapE,AFUA_4G08340"]), # AFUA_4G08340 is COX10 according to MARDy
             docker = snippy_gene_query_docker_image
         }
       }
-    }
     if (merlin_tag == "Cryptococcus neoformans") {
       if (!assembly_only && !ont_data) {
         call snippy.snippy_variants as snippy_crypto {
@@ -723,16 +739,31 @@ workflow merlin_magic {
             maxsoft = snippy_maxsoft,
             docker = snippy_variants_docker_image
         }
+      }
+      if (assembly_only && ont_data) {
+        call snippy.snippy_variants as snippy_crypto_ont {
+          input:
+            reference_genome_file = snippy_reference_cryptoneo,
+            assembly_fasta = assembly,
+            samplename = samplename,
+            map_qual = snippy_map_qual,
+            base_quality = snippy_base_quality,
+            min_coverage = snippy_min_coverage,
+            min_frac = snippy_min_frac,
+            min_quality = snippy_min_quality,
+            maxsoft = snippy_maxsoft,
+            docker = snippy_variants_docker_image
+        }
+      }
         call snippy_gene_query.snippy_gene_query as snippy_gene_query_crypto {
           input:
             samplename = samplename,
-            snippy_variants_results = snippy_crypto.snippy_variants_results,
+            snippy_variants_results = select_first([snippy_crypto.snippy_variants_results, snippy_crypto_ont.snippy_variants_results]),
             reference = snippy_reference_cryptoneo,
             query_gene = select_first([snippy_query_gene, "CNA00300"]), # CNA00300 is ERG11 for this reference genome
             docker = snippy_gene_query_docker_image
         }
       }
-    }
   }
   output {
     # theiaprok
@@ -983,20 +1014,20 @@ workflow merlin_magic {
     String? cladetyper_docker_image = cladetyper.gambit_cladetyper_docker_image
     String? cladetype_annotated_ref = cladetyper.clade_spec_ref
     # snippy variants
-    String snippy_variants_reference_genome = select_first([snippy_cauris.snippy_variants_reference_genome, snippy_cauris_ont.snippy_variants_reference_genome, snippy_afumigatus.snippy_variants_reference_genome, snippy_crypto.snippy_variants_reference_genome, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_version = select_first([snippy_cauris.snippy_variants_version, snippy_cauris_ont.snippy_variants_version,snippy_afumigatus.snippy_variants_version, snippy_crypto.snippy_variants_version, "No matching taxon detected"])
+    String snippy_variants_reference_genome = select_first([snippy_cauris.snippy_variants_reference_genome, snippy_cauris_ont.snippy_variants_reference_genome, snippy_afumigatus.snippy_variants_reference_genome, snippy_afumigatus_ont.snippy_variants_reference_genome, snippy_crypto.snippy_variants_reference_genome, snippy_crypto_ont.snippy_variants_reference_genome, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_version = select_first([snippy_cauris.snippy_variants_version, snippy_cauris_ont.snippy_variants_version,snippy_afumigatus.snippy_variants_version, snippy_afumigatus_ont.snippy_variants_version, snippy_crypto.snippy_variants_version, snippy_crypto_ont.snippy_variants_version, "No matching taxon detected"])
     String snippy_variants_query = select_first([snippy_gene_query_cauris.snippy_variants_query, snippy_gene_query_afumigatus.snippy_variants_query, snippy_gene_query_crypto.snippy_variants_query, "No matching taxon detected"])
     String snippy_variants_query_check = select_first([snippy_gene_query_cauris.snippy_variants_query_check, snippy_gene_query_afumigatus.snippy_variants_query_check, snippy_gene_query_crypto.snippy_variants_query_check, "No matching taxon detected"])
     String snippy_variants_hits = select_first([snippy_gene_query_cauris.snippy_variants_hits, snippy_gene_query_afumigatus.snippy_variants_hits, snippy_gene_query_crypto.snippy_variants_hits, "No matching taxon detected"])
     String snippy_variants_gene_query_results = select_first([snippy_gene_query_cauris.snippy_variants_gene_query_results, snippy_gene_query_afumigatus.snippy_variants_gene_query_results, snippy_gene_query_crypto.snippy_variants_gene_query_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_outdir_tarball = select_first([snippy_cauris.snippy_variants_outdir_tarball, snippy_cauris_ont.snippy_variants_outdir_tarball, snippy_afumigatus.snippy_variants_outdir_tarball, snippy_crypto.snippy_variants_outdir_tarball, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_results = select_first([snippy_cauris.snippy_variants_results, snippy_cauris_ont.snippy_variants_results,snippy_afumigatus.snippy_variants_results, snippy_crypto.snippy_variants_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_bam = select_first([snippy_cauris.snippy_variants_bam, snippy_cauris_ont.snippy_variants_bam, snippy_afumigatus.snippy_variants_bam, snippy_crypto.snippy_variants_bam, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_bai = select_first([snippy_cauris.snippy_variants_bai, snippy_cauris_ont.snippy_variants_bai, snippy_afumigatus.snippy_variants_bai, snippy_crypto.snippy_variants_bai, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_summary = select_first([snippy_cauris.snippy_variants_summary, snippy_cauris_ont.snippy_variants_summary, snippy_afumigatus.snippy_variants_summary, snippy_crypto.snippy_variants_summary, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_num_reads_aligned = select_first([snippy_cauris.snippy_variants_num_reads_aligned, snippy_cauris_ont.snippy_variants_num_reads_aligned, snippy_afumigatus.snippy_variants_num_reads_aligned, snippy_crypto.snippy_variants_num_reads_aligned, "No matching taxon detected"])
-    String snippy_variants_coverage_tsv = select_first([snippy_cauris.snippy_variants_coverage_tsv, snippy_cauris_ont.snippy_variants_coverage_tsv, snippy_afumigatus.snippy_variants_coverage_tsv, snippy_crypto.snippy_variants_coverage_tsv, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
-    String snippy_variants_num_variants = select_first([snippy_cauris.snippy_variants_num_variants, snippy_cauris_ont.snippy_variants_num_variants, snippy_afumigatus.snippy_variants_num_variants, snippy_crypto.snippy_variants_num_reads_aligned, "No matching taxon detected"])
-    String snippy_variants_percent_ref_coverage = select_first([snippy_cauris.snippy_variants_percent_ref_coverage, snippy_cauris_ont.snippy_variants_percent_ref_coverage, snippy_afumigatus.snippy_variants_percent_ref_coverage, snippy_crypto.snippy_variants_percent_ref_coverage, "No matching taxon detected"])
+    String snippy_variants_outdir_tarball = select_first([snippy_cauris.snippy_variants_outdir_tarball, snippy_cauris_ont.snippy_variants_outdir_tarball, snippy_afumigatus.snippy_variants_outdir_tarball, snippy_afumigatus_ont.snippy_variants_outdir_tarball, snippy_crypto.snippy_variants_outdir_tarball, snippy_crypto_ont.snippy_variants_outdir_tarball, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_results = select_first([snippy_cauris.snippy_variants_results, snippy_cauris_ont.snippy_variants_results,snippy_afumigatus.snippy_variants_results, snippy_afumigatus_ont.snippy_variants_results, snippy_crypto.snippy_variants_results, snippy_crypto_ont.snippy_variants_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_bam = select_first([snippy_cauris.snippy_variants_bam, snippy_cauris_ont.snippy_variants_bam, snippy_afumigatus.snippy_variants_bam, snippy_afumigatus_ont.snippy_variants_bam, snippy_crypto.snippy_variants_bam, snippy_crypto_ont.snippy_variants_bam, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_bai = select_first([snippy_cauris.snippy_variants_bai, snippy_cauris_ont.snippy_variants_bai, snippy_afumigatus.snippy_variants_bai, snippy_afumigatus_ont.snippy_variants_bai, snippy_crypto.snippy_variants_bai, snippy_crypto_ont.snippy_variants_bai, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_summary = select_first([snippy_cauris.snippy_variants_summary, snippy_cauris_ont.snippy_variants_summary, snippy_afumigatus.snippy_variants_summary, snippy_afumigatus_ont.snippy_variants_summary, snippy_crypto.snippy_variants_summary, snippy_crypto_ont.snippy_variants_summary, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_num_reads_aligned = select_first([snippy_cauris.snippy_variants_num_reads_aligned, snippy_cauris_ont.snippy_variants_num_reads_aligned, snippy_afumigatus.snippy_variants_num_reads_aligned, snippy_afumigatus_ont.snippy_variants_num_reads_aligned, snippy_crypto.snippy_variants_num_reads_aligned, snippy_crypto_ont.snippy_variants_num_reads_aligned, "No matching taxon detected"])
+    String snippy_variants_coverage_tsv = select_first([snippy_cauris.snippy_variants_coverage_tsv, snippy_cauris_ont.snippy_variants_coverage_tsv, snippy_afumigatus.snippy_variants_coverage_tsv, snippy_afumigatus_ont.snippy_variants_coverage_tsv, snippy_crypto.snippy_variants_coverage_tsv, snippy_crypto_ont.snippy_variants_coverage_tsv, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
+    String snippy_variants_num_variants = select_first([snippy_cauris.snippy_variants_num_variants, snippy_cauris_ont.snippy_variants_num_variants, snippy_afumigatus.snippy_variants_num_variants, snippy_afumigatus_ont.snippy_variants_num_variants, snippy_crypto.snippy_variants_num_reads_aligned, snippy_crypto_ont.snippy_variants_num_variants, "No matching taxon detected"])
+    String snippy_variants_percent_ref_coverage = select_first([snippy_cauris.snippy_variants_percent_ref_coverage, snippy_cauris_ont.snippy_variants_percent_ref_coverage, snippy_afumigatus.snippy_variants_percent_ref_coverage, snippy_afumigatus_ont.snippy_variants_percent_ref_coverage, snippy_crypto.snippy_variants_percent_ref_coverage, snippy_crypto_ont.snippy_variants_percent_ref_coverage, "No matching taxon detected"])
   }
 }
\ No newline at end of file

From e23e9ab9255fb4ca3a5614162751cfd3d683bf29 Mon Sep 17 00:00:00 2001
From: Michal-Babins <michal.babinski@theiagen.com>
Date: Fri, 18 Oct 2024 18:41:54 +0000
Subject: [PATCH 13/13] updated md5 sum for merlin magic

---
 tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml | 2 +-
 tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
index bae74e2e5..fc163f307 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -633,7 +633,7 @@
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
       md5sum: 6d9dd969e2144ca23f2a0e101e6b6966
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
-      md5sum: ba96a542bb0896569fee6136f712fdd1
+      md5sum: 75f2c3825fcce2931d7c37c3bdbd74b8
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_pe.wdl
       contains: ["version", "QC", "output"]
     - path: miniwdl_run/workflow.log
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
index 3a891aaa8..a23424aa7 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -596,7 +596,7 @@
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
       md5sum: 5aa25e4fad466f92c96a7c138aca0d20
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
-      md5sum: ba96a542bb0896569fee6136f712fdd1
+      md5sum: 75f2c3825fcce2931d7c37c3bdbd74b8
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl
       md5sum: d11bfe33fdd96eab28892be5a01c1c7d
     - path: miniwdl_run/workflow.log