From 85021130c18e86d66c332fdf6768e22f782c57e7 Mon Sep 17 00:00:00 2001
From: Kasper Thystrup Karstensen <kathka@gmail.com>
Date: Fri, 3 Jul 2026 13:34:17 +0200
Subject: [PATCH 01/13] Add CPO.yaml configuration

---
 src/mmaseq/config/species_configs/CPO.yaml | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 src/mmaseq/config/species_configs/CPO.yaml

diff --git a/src/mmaseq/config/species_configs/CPO.yaml b/src/mmaseq/config/species_configs/CPO.yaml
new file mode 100644
index 0000000..9d3d9ee
--- /dev/null
+++ b/src/mmaseq/config/species_configs/CPO.yaml
@@ -0,0 +1,8 @@
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
+
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm

From 244c228d4708779f46d0b579dab9f53ffc273704 Mon Sep 17 00:00:00 2001
From: Kasper Thystrup Karstensen <kathka@gmail.com>
Date: Fri, 3 Jul 2026 13:41:51 +0200
Subject: [PATCH 02/13] Refactor E_coli.yaml configuration for tools

---
 src/mmaseq/config/species_configs/E_coli.yaml | 42 ++++++++-----------
 1 file changed, 17 insertions(+), 25 deletions(-)

diff --git a/src/mmaseq/config/species_configs/E_coli.yaml b/src/mmaseq/config/species_configs/E_coli.yaml
index d048799..ded178f 100644
--- a/src/mmaseq/config/species_configs/E_coli.yaml
+++ b/src/mmaseq/config/species_configs/E_coli.yaml
@@ -1,37 +1,29 @@
-kmeraligner_wrangler:
-    options: --organism 'Escherichia coli'
-    database: ecoligenes
-
 resfinder:
     options: --species 'Escherichia coli'
+    assembler: shovill
 
 pointfinder:
     options: --species 'Escherichia coli'
+    assembler: shovill
 
-disinfinder:
-    options: --species 'Escherichia coli'
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
 
-plasmidfinder: true
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
 
-virulencefinder: true
+virulencefinder: 
+    assembler: shovill
 
-serotypefinder: true
+serotypefinder:
+    reads: True
 
-amrfinder:
-    options: --organism 'Escherichia'
-    assembler: shovill 
+kmeraligner_wrangler:
+    options: --organism 'Escherichia coli'
+    database: ecoligenes
 
 chtyper:
-    database: fumCH_db 
-
-mlst:
-    assembler: shovill  
-
-blastn:
-    options: "-perc_identity 90.0"
-    assembler: shovill
-    database : OXAndm
-
-kleborate:
-    options: --preset escherichia
-    assembler: shovill
+    database: fumCH_db

From 6e7f68654147edaeb025aadca57613e0c35a14f5 Mon Sep 17 00:00:00 2001
From: Kasper Thystrup Karstensen <kathka@gmail.com>
Date: Fri, 3 Jul 2026 13:45:25 +0200
Subject: [PATCH 03/13] Refactored E_Faecium.yaml configuration settings

Updated configuration for plasmidfinder, blastn, pointfinder, and kmeraligner.
---
 .../config/species_configs/E_Faecium.yaml     | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/mmaseq/config/species_configs/E_Faecium.yaml b/src/mmaseq/config/species_configs/E_Faecium.yaml
index 3265749..0248756 100644
--- a/src/mmaseq/config/species_configs/E_Faecium.yaml
+++ b/src/mmaseq/config/species_configs/E_Faecium.yaml
@@ -1,15 +1,15 @@
-plasmidfinder: true
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
 
-virulencefinder: true
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
 
-serotypefinder: true
-
-amrfinder:
-    options: --organism 'Enterococcus_faecium'
-    assembler: [shovill]  
-
-mlst:
-    assembler: [shovill]  
+pointfinder:
+    options: --species 'enterococcus faecium'
+    assembler: shovill
 
 lrefinder:
     database : [elmDB]

From f54c2fccf93e5d005a3b50ad8251399ced732dfc Mon Sep 17 00:00:00 2001
From: Kasper Thystrup Karstensen <kathka@gmail.com>
Date: Fri, 3 Jul 2026 13:45:49 +0200
Subject: [PATCH 04/13] Refactored E_Faecalis.yaml configuration settings

---
 .../config/species_configs/E_Faecalis.yaml    | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/mmaseq/config/species_configs/E_Faecalis.yaml b/src/mmaseq/config/species_configs/E_Faecalis.yaml
index f93ac55..5756011 100644
--- a/src/mmaseq/config/species_configs/E_Faecalis.yaml
+++ b/src/mmaseq/config/species_configs/E_Faecalis.yaml
@@ -1,15 +1,15 @@
-plasmidfinder: true
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
 
-virulencefinder: true
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
 
-serotypefinder: true
-
-amrfinder:
-    options: --organism 'Enterococcus_faecalis'
-    assembler: [shovill]  
-
-mlst:
-    assembler: [shovill]  
+pointfinder:
+    options: --species 'Enterococcus faecalis'
+    assembler: shovill
 
 lrefinder:
     database : [elmDB]

From bd0973c8c04830f5a6e089daee7c4f9f61dccea3 Mon Sep 17 00:00:00 2001
From: Kasper Thystrup Karstensen <kathka@gmail.com>
Date: Fri, 3 Jul 2026 13:46:02 +0200
Subject: [PATCH 05/13] Correct species name casing in E_Faecium.yaml

---
 src/mmaseq/config/species_configs/E_Faecium.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mmaseq/config/species_configs/E_Faecium.yaml b/src/mmaseq/config/species_configs/E_Faecium.yaml
index 0248756..a06efa3 100644
--- a/src/mmaseq/config/species_configs/E_Faecium.yaml
+++ b/src/mmaseq/config/species_configs/E_Faecium.yaml
@@ -8,7 +8,7 @@ blastn:
   database : OXAndm
 
 pointfinder:
-    options: --species 'enterococcus faecium'
+    options: --species 'Enterococcus faecium'
     assembler: shovill
 
 lrefinder:

From 2facb9fe191e03e1a9773463e56a0b2536e6bd08 Mon Sep 17 00:00:00 2001
From: SimoneScrima <simonescrima@gmail.com>
Date: Fri, 3 Jul 2026 14:32:56 +0200
Subject: [PATCH 06/13] New species

---
 src/mmaseq/config/species_configs/C_coli.yaml | 12 ++++++++++
 .../config/species_configs/C_jejuni.yaml      | 12 ++++++++++
 .../config/species_configs/Campylobacter.yaml | 12 ++++++++++
 .../config/species_configs/H_pylori.yaml      | 12 ++++++++++
 .../{K_pneumoniae.yaml => Klebsiella.yaml}    |  9 +++++++-
 .../species_configs/M_tuberculosis.yaml       |  8 +++++++
 .../config/species_configs/N_gonorrhoeae.yaml | 12 ++++++++++
 .../species_configs/N_meningitidis.yaml       |  9 +++++++-
 .../config/species_configs/S_aureus.yaml      |  2 +-
 .../config/species_configs/S_enterica.yaml    | 21 -----------------
 .../config/species_configs/Salmonella.yaml    | 23 +++++++++++++++++++
 11 files changed, 108 insertions(+), 24 deletions(-)
 create mode 100644 src/mmaseq/config/species_configs/C_coli.yaml
 create mode 100644 src/mmaseq/config/species_configs/C_jejuni.yaml
 create mode 100644 src/mmaseq/config/species_configs/Campylobacter.yaml
 create mode 100644 src/mmaseq/config/species_configs/H_pylori.yaml
 rename src/mmaseq/config/species_configs/{K_pneumoniae.yaml => Klebsiella.yaml} (72%)
 create mode 100644 src/mmaseq/config/species_configs/M_tuberculosis.yaml
 create mode 100644 src/mmaseq/config/species_configs/N_gonorrhoeae.yaml
 delete mode 100644 src/mmaseq/config/species_configs/S_enterica.yaml
 create mode 100644 src/mmaseq/config/species_configs/Salmonella.yaml

diff --git a/src/mmaseq/config/species_configs/C_coli.yaml b/src/mmaseq/config/species_configs/C_coli.yaml
new file mode 100644
index 0000000..2bb22c2
--- /dev/null
+++ b/src/mmaseq/config/species_configs/C_coli.yaml
@@ -0,0 +1,12 @@
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
+
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
+  
+pointfinder:
+    options: --species 'Campylobacter coli'
+    assembler: shovill
\ No newline at end of file
diff --git a/src/mmaseq/config/species_configs/C_jejuni.yaml b/src/mmaseq/config/species_configs/C_jejuni.yaml
new file mode 100644
index 0000000..6175709
--- /dev/null
+++ b/src/mmaseq/config/species_configs/C_jejuni.yaml
@@ -0,0 +1,12 @@
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
+
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
+
+pointfinder:
+    options: --species 'Campylobacter jejuni'
+    assembler: shovill
\ No newline at end of file
diff --git a/src/mmaseq/config/species_configs/Campylobacter.yaml b/src/mmaseq/config/species_configs/Campylobacter.yaml
new file mode 100644
index 0000000..2bb22c2
--- /dev/null
+++ b/src/mmaseq/config/species_configs/Campylobacter.yaml
@@ -0,0 +1,12 @@
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
+
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
+  
+pointfinder:
+    options: --species 'Campylobacter coli'
+    assembler: shovill
\ No newline at end of file
diff --git a/src/mmaseq/config/species_configs/H_pylori.yaml b/src/mmaseq/config/species_configs/H_pylori.yaml
new file mode 100644
index 0000000..c335684
--- /dev/null
+++ b/src/mmaseq/config/species_configs/H_pylori.yaml
@@ -0,0 +1,12 @@
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
+
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
+
+pointfinder:
+    options: --species 'Helicobacter pylori'
+    assembler: shovill
\ No newline at end of file
diff --git a/src/mmaseq/config/species_configs/K_pneumoniae.yaml b/src/mmaseq/config/species_configs/Klebsiella.yaml
similarity index 72%
rename from src/mmaseq/config/species_configs/K_pneumoniae.yaml
rename to src/mmaseq/config/species_configs/Klebsiella.yaml
index dddaefc..d9da3ae 100644
--- a/src/mmaseq/config/species_configs/K_pneumoniae.yaml
+++ b/src/mmaseq/config/species_configs/Klebsiella.yaml
@@ -1,4 +1,11 @@
-plasmidfinder: true
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
+
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
 
 resfinder:
     options: --species 'Klebsiella'
diff --git a/src/mmaseq/config/species_configs/M_tuberculosis.yaml b/src/mmaseq/config/species_configs/M_tuberculosis.yaml
new file mode 100644
index 0000000..9d3d9ee
--- /dev/null
+++ b/src/mmaseq/config/species_configs/M_tuberculosis.yaml
@@ -0,0 +1,8 @@
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
+
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
diff --git a/src/mmaseq/config/species_configs/N_gonorrhoeae.yaml b/src/mmaseq/config/species_configs/N_gonorrhoeae.yaml
new file mode 100644
index 0000000..63d17cd
--- /dev/null
+++ b/src/mmaseq/config/species_configs/N_gonorrhoeae.yaml
@@ -0,0 +1,12 @@
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
+
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
+
+pointfinder:
+    options: --species 'Neisseria gonorrhoeae'
+    assembler: shovill
\ No newline at end of file
diff --git a/src/mmaseq/config/species_configs/N_meningitidis.yaml b/src/mmaseq/config/species_configs/N_meningitidis.yaml
index 83842d7..ba2c014 100644
--- a/src/mmaseq/config/species_configs/N_meningitidis.yaml
+++ b/src/mmaseq/config/species_configs/N_meningitidis.yaml
@@ -1,4 +1,11 @@
-plasmidfinder: true
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
+
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
 
 virulencefinder: true
 
diff --git a/src/mmaseq/config/species_configs/S_aureus.yaml b/src/mmaseq/config/species_configs/S_aureus.yaml
index 7866e0d..e616eed 100644
--- a/src/mmaseq/config/species_configs/S_aureus.yaml
+++ b/src/mmaseq/config/species_configs/S_aureus.yaml
@@ -1,2 +1,2 @@
 spatyper:
-  assembler: [spades]
+  assembler: [spades]
\ No newline at end of file
diff --git a/src/mmaseq/config/species_configs/S_enterica.yaml b/src/mmaseq/config/species_configs/S_enterica.yaml
deleted file mode 100644
index 18a627e..0000000
--- a/src/mmaseq/config/species_configs/S_enterica.yaml
+++ /dev/null
@@ -1,21 +0,0 @@
-resfinder:
-  options: --species 'Salmonella enterica'
-
-pointfinder:
-  options: --species 'Salmonella enterica'
-
-disinfinder:
-  options: --species 'Salmonella enterica'
-
-
-amrfinder:
-  options: --organism 'Salmonella'
-  assembler: shovill
-  
-mlst:
-  assembler: shovill
-
-seqsero2: true
-
-sistr:
-  assembler: shovill
diff --git a/src/mmaseq/config/species_configs/Salmonella.yaml b/src/mmaseq/config/species_configs/Salmonella.yaml
new file mode 100644
index 0000000..49a2468
--- /dev/null
+++ b/src/mmaseq/config/species_configs/Salmonella.yaml
@@ -0,0 +1,23 @@
+pointfinder:
+    options: --species 'Salmonella'
+    assembler: shovill
+
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
+
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
+
+amrfinder:
+  options: --organism 'Salmonella'
+  assembler: shovill
+
+seqsero2: 
+  reads
+
+sistr:
+  assembler: shovill
+

From c7e64c812751a5c0c1e31a5e4c3065ec1cb7cb44 Mon Sep 17 00:00:00 2001
From: "simonescrima@gmail.com" <simonescrima@gmail.com>
Date: Mon, 20 Jul 2026 11:15:32 +0200
Subject: [PATCH 07/13] Added retries for curl when failing

---
 src/mmaseq/workflow/rules/Databases.smk | 34 ++++++++++++++-----------
 1 file changed, 19 insertions(+), 15 deletions(-)

diff --git a/src/mmaseq/workflow/rules/Databases.smk b/src/mmaseq/workflow/rules/Databases.smk
index 877c41c..ff060d1 100644
--- a/src/mmaseq/workflow/rules/Databases.smk
+++ b/src/mmaseq/workflow/rules/Databases.smk
@@ -62,8 +62,8 @@ rule fetch_type_repeat_sequence:
         fasta_url="https://raw.githubusercontent.com/ssi-dk/ssi_analysis_utility_db/main/$rel_path"
         ver_url="https://raw.githubusercontent.com/ssi-dk/ssi_analysis_utility_db/main/$rel_ver"
 
-        cmd_fasta="curl -fSL $fasta_url -o {output.seq}"
-        cmd_ver="curl -fSL $ver_url -o {output.version_db}"
+        cmd_fasta="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $fasta_url -o {output.seq}"
+        cmd_ver="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $ver_url -o {output.version_db}"
 
         echo "Executing command:\n$cmd_fasta\n$cmd_ver\n" > {log.stdout}
         eval "$cmd_fasta" >> {log.stdout} 2>&1
@@ -84,7 +84,7 @@ rule fetch_type_repeat_metadata:
         """
         mkdir -p $(dirname {output.meta})
 
-        cmd="curl -fSL https://raw.githubusercontent.com/ssi-dk/ssi_analysis_utility_db/refs/heads/main/clostridioides_difficile/type_repeats/{wildcards.TR}.txt -o {output.meta}"
+        cmd="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors https://raw.githubusercontent.com/ssi-dk/ssi_analysis_utility_db/refs/heads/main/clostridioides_difficile/type_repeats/{wildcards.TR}.txt -o {output.meta}"
 
         echo "Executing command:\n$cmd\n" > {log.stdout}
         eval $cmd >> {log.stdout} 2>&1
@@ -112,8 +112,8 @@ rule fetch_ecoligenes:
         fasta_url="https://raw.githubusercontent.com/ssi-dk/ssi_analysis_utility_db/main/$rel_path"
         ver_url="https://raw.githubusercontent.com/ssi-dk/ssi_analysis_utility_db/main/$rel_ver"
 
-        cmd_fasta="curl -fSL $fasta_url -o {output.source}"
-        cmd_ver="curl -fSL $ver_url | awk '1' > {output.version_db}"
+        cmd_fasta="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $fasta_url -o {output.source}"
+        cmd_ver="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $ver_url | awk '1' > {output.version_db}"
 
         echo "Executing command:\n$cmd_fasta\n$cmd_ver\n" > {log.stdout}
         eval "$cmd_fasta" >> {log.stdout} 2>&1
@@ -140,8 +140,8 @@ rule fetch_senterica_scheme:
         fasta_url="https://enterobase.warwick.ac.uk/schemes/Salmonella.Achtman7GeneMLST/MLST_Achtman_ref.fasta"
         profile_url="https://enterobase.warwick.ac.uk/schemes/Salmonella.Achtman7GeneMLST/profiles.list.gz"
 
-        fasta_cmd="curl -fSL $fasta_url -o {output.source}"
-        profile_cmd="curl -fSL $profile_url -o {output.profile}"
+        fasta_cmd="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $fasta_url -o {output.source}"
+        profile_cmd="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $profile_url -o {output.profile}"
 
         echo "Executing command:\n$fasta_cmd\n" > {log.stdout} 2>&1
         eval $fasta_cmd >> {log.stdout} 2>&1
@@ -189,7 +189,7 @@ rule fetch_senterica_serovar:
         list_url="https://raw.githubusercontent.com/phac-nml/sistr_cmd/master/sistr/data/serovar-list.txt"
 
         # 1) Download the serovar list
-        cmd_fasta="curl -fSL $list_url -o {output.source}"
+        cmd_fasta="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $list_url -o {output.source}"
 
         echo "Executing command:\n$cmd_fasta\n" > {log.stdout}
         eval "$cmd_fasta" >> {log.stdout} 2>&1
@@ -239,8 +239,8 @@ rule fetch_chtyper_db:
         fumC_url="https://bitbucket.org/genomicepidemiology/chtyper_db/raw/654ca48d250e0a69c6c06b4be5a96d807b23f806/fumC.fsa"
 
         # 1) Download the serovar list
-        cmd_fimH="curl -fSL $fimH_url -o $outdir/fimH.fsa"
-        cmd_fumC="curl -fSL $fumC_url -o $outdir/fumC.fsa"
+        cmd_fimH="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $fimH_url -o $outdir/fimH.fsa"
+        cmd_fumC="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $fumC_url -o $outdir/fumC.fsa"
 
         echo "Executing command:\n$cmd_fimH\n" > {log.stdout}
         eval "$cmd_fimH" >> {log.stdout} 2>&1
@@ -286,8 +286,8 @@ rule fetch_custom_blast_database:
         fasta_url="https://raw.githubusercontent.com/ssi-dk/ssi_analysis_utility_db/main/$rel_path"
         ver_url="https://raw.githubusercontent.com/ssi-dk/ssi_analysis_utility_db/main/$rel_ver"
 
-        cmd_fasta="curl -fSL $fasta_url -o {output.source}"
-        cmd_ver="curl -fSL $ver_url  | awk '1' > {output.version_db}"
+        cmd_fasta="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $fasta_url -o {output.source}"
+        cmd_ver="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $ver_url  | awk '1' > {output.version_db}"
 
         echo "Executing command:\n$cmd_fasta\n$cmd_ver\n" > {log.stdout}
         eval "$cmd_fasta" >> {log.stdout} 2>&1
@@ -300,6 +300,8 @@ rule fetch_vancomycin:
         source = f"{database_dir}/custom/vancomycin.fasta"
     log:
         stdout = f"{logdir}/Databases/fetch_vancomycin.log"
+    conda:
+        ENVS_DIR / "blast.yaml"    
     message:
         "[fetch_vancomycin]: Downloading custom vancomycin database"
     shell:
@@ -310,7 +312,7 @@ rule fetch_vancomycin:
                 
         fasta_url="https://raw.githubusercontent.com/ssi-dk/ssi_analysis_utility_db/refs/heads/main/resistance/vancomycin.fasta"
 
-        cmd="curl -fSL $fasta_url -o {output.source}"
+        cmd="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $fasta_url -o {output.source}"
 
         echo "Executing command:\n$cmd\n" > {log.stdout}
         eval "$cmd" >> {log.stdout} 2>&1
@@ -322,6 +324,8 @@ rule fetch_vancomycin_operon:
         source = f"{database_dir}/custom/vancomycinOperon.fasta"
     log:
         stdout = f"{logdir}/Databases/fetch_vancomycin_operon.log"
+    conda:
+        ENVS_DIR / "blast.yaml" 
     message:
         "[fetch_vancomycin_operon]: Downloading custom vancomycin operon database"
     shell:
@@ -332,7 +336,7 @@ rule fetch_vancomycin_operon:
                 
         fasta_url="https://raw.githubusercontent.com/ssi-dk/ssi_analysis_utility_db/refs/heads/main/resistance/vancomycinOperon.fasta"
 
-        cmd="curl -fSL $fasta_url -o {output.source}"
+        cmd="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $fasta_url -o {output.source}"
 
         echo "Executing command:\n$cmd\n" > {log.stdout}
         eval "$cmd" >> {log.stdout} 2>&1
@@ -819,7 +823,7 @@ rule setup_lrefinder:
         sequence_url="https://bitbucket.org/genomicepidemiology/lre-finder/raw/fac445d190853cc90c1aed392a55102fe9df4376/elmDB.tar.gz"
 
         # 1) download raw sequence
-        cmd="curl -fSL $sequence_url --output - | tar -xzvf - -C {params.prefix} && mv {params.dbdir}elm.fsa {output.source} && rm -rf {params.dbdir}"
+        cmd="curl -fSL --retry 5 --retry-delay 3 --retry-all-errors $sequence_url --output - | tar -xzvf - -C {params.prefix} && mv {params.dbdir}elm.fsa {output.source} && rm -rf {params.dbdir}"
 
         echo -e "Executing command:\n$cmd\n" > {log.stdout} 2>&1
         eval $cmd >> {log.stdout} 2>&1

From 1b8bfea7efcbb5c66a4fb8b791c0ec16c5e48425 Mon Sep 17 00:00:00 2001
From: SimoneScrima <simonescrima@gmail.com>
Date: Mon, 20 Jul 2026 13:37:18 +0200
Subject: [PATCH 08/13] Splitted klebsiella in oxytoca and pneumoniae since it
 amrfinderplus support those individually

---
 .../config/species_configs/K_oxytoca.yaml     | 37 +++++++++++++++++++
 .../{Klebsiella.yaml => K_pneumoniae.yaml}    |  0
 src/mmaseq/data/samplesheet.tsv               |  2 +-
 3 files changed, 38 insertions(+), 1 deletion(-)
 create mode 100644 src/mmaseq/config/species_configs/K_oxytoca.yaml
 rename src/mmaseq/config/species_configs/{Klebsiella.yaml => K_pneumoniae.yaml} (100%)

diff --git a/src/mmaseq/config/species_configs/K_oxytoca.yaml b/src/mmaseq/config/species_configs/K_oxytoca.yaml
new file mode 100644
index 0000000..b9b04b1
--- /dev/null
+++ b/src/mmaseq/config/species_configs/K_oxytoca.yaml
@@ -0,0 +1,37 @@
+plasmidfinder:
+  options: "-l 80 -t 80"
+  assembler: shovill
+
+blastn:
+  options: "-perc_identity 99.0"
+  assembler: shovill
+  database : OXAndm
+
+resfinder:
+    options: --species 'Klebsiella'
+    reads: True
+
+pointfinder:
+    options: --species 'Klebsiella'
+    reads: True
+
+disinfinder:
+    options: --species 'Klebsiella'
+    reads: True
+
+virulencefinder:
+    reads: True
+
+serotypefinder:
+    reads: True
+
+amrfinder:
+    options: --organism 'Klebsiella_oxytoca'
+    assembler: shovill 
+
+kleborate:
+    options: --preset kpsc
+    assembler: shovill
+
+mlst:
+    assembler: shovill  
diff --git a/src/mmaseq/config/species_configs/Klebsiella.yaml b/src/mmaseq/config/species_configs/K_pneumoniae.yaml
similarity index 100%
rename from src/mmaseq/config/species_configs/Klebsiella.yaml
rename to src/mmaseq/config/species_configs/K_pneumoniae.yaml
diff --git a/src/mmaseq/data/samplesheet.tsv b/src/mmaseq/data/samplesheet.tsv
index 9d872b0..e66623c 100755
--- a/src/mmaseq/data/samplesheet.tsv
+++ b/src/mmaseq/data/samplesheet.tsv
@@ -2,7 +2,7 @@ sample_name	read1	read2	assembly	config
 ERR3528110	reads/ERR3528110_1.fastq.gz	reads/ERR3528110_2.fastq.gz	assemblies/ERR3528110.fasta	E_coli.yaml
 SRR4046826	reads/SRR4046826_1.fastq.gz	reads/SRR4046826_2.fastq.gz	assemblies/SRR4046826.fasta	K_pneumoniae.yaml
 SRR25448586	reads/SRR25448586_1.fastq.gz	reads/SRR25448586_2.fastq.gz	assemblies/SRR25448586.fasta	N_meningitidis.yaml
-SRR26205262	reads/SRR26205262_1.fastq.gz	reads/SRR26205262_2.fastq.gz	assemblies/SRR26205262.fasta	S_enterica.yaml
+SRR26205262	reads/SRR26205262_1.fastq.gz	reads/SRR26205262_2.fastq.gz	assemblies/SRR26205262.fasta	Samonella.yaml
 ERR2929615	reads/ERR2929615_1.fastq.gz	reads/ERR2929615_2.fastq.gz	assemblies/ERR2929615.fasta	E_Faecalis.yaml
 ERR2929578	reads/ERR2929578_1.fastq.gz	reads/ERR2929578_2.fastq.gz	assemblies/ERR2929578.fasta	E_Faecium.yaml
 ERR142064	reads/ERR142064_1.fastq.gz	reads/ERR142064_2.fastq.gz	assemblies/ERR142064.fasta	C_difficile.yaml

From 109ca24561f8909dad74682d23e34e30f6dc5454 Mon Sep 17 00:00:00 2001
From: "simonescrima@gmail.com" <simonescrima@gmail.com>
Date: Mon, 20 Jul 2026 14:34:46 +0200
Subject: [PATCH 09/13] Fixed errors in the configs

---
 src/mmaseq/config/species_configs/E_coli.yaml  |  1 +
 src/mmaseq/config/species_configs/default.yaml | 10 +++++++---
 src/mmaseq/data/samplesheet.tsv                |  2 +-
 src/mmaseq/utils/sample_config.py              | 14 ++++++++------
 4 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/src/mmaseq/config/species_configs/E_coli.yaml b/src/mmaseq/config/species_configs/E_coli.yaml
index 5dd3251..d652105 100644
--- a/src/mmaseq/config/species_configs/E_coli.yaml
+++ b/src/mmaseq/config/species_configs/E_coli.yaml
@@ -24,6 +24,7 @@ serotypefinder:
 kmeraligner_wrangler:
     options: --organism 'Escherichia coli'
     database: ecoligenes
+    reads: True
 
 chtyper:
     database: fumCH 
diff --git a/src/mmaseq/config/species_configs/default.yaml b/src/mmaseq/config/species_configs/default.yaml
index da81e57..e1e3e81 100644
--- a/src/mmaseq/config/species_configs/default.yaml
+++ b/src/mmaseq/config/species_configs/default.yaml
@@ -7,20 +7,24 @@ resfinder:
 
 plasmidfinder:
     options: ""
+    reads: True
 
 virulencefinder:
     options: ""
+    reads: True
 
 serotypefinder:
     options: ""
-          
+    reads: True
+
 amrfinder:
     assembler: shovill
     options: ""
-    
+
 meningotype:
     assembler: shovill
 
 kmeraligner:
     database: elmDB
-    options : -ID 80 -1t1 -cge
\ No newline at end of file
+    options : -ID 80 -1t1 -cge
+    reads: True
\ No newline at end of file
diff --git a/src/mmaseq/data/samplesheet.tsv b/src/mmaseq/data/samplesheet.tsv
index e66623c..3c057c6 100755
--- a/src/mmaseq/data/samplesheet.tsv
+++ b/src/mmaseq/data/samplesheet.tsv
@@ -2,7 +2,7 @@ sample_name	read1	read2	assembly	config
 ERR3528110	reads/ERR3528110_1.fastq.gz	reads/ERR3528110_2.fastq.gz	assemblies/ERR3528110.fasta	E_coli.yaml
 SRR4046826	reads/SRR4046826_1.fastq.gz	reads/SRR4046826_2.fastq.gz	assemblies/SRR4046826.fasta	K_pneumoniae.yaml
 SRR25448586	reads/SRR25448586_1.fastq.gz	reads/SRR25448586_2.fastq.gz	assemblies/SRR25448586.fasta	N_meningitidis.yaml
-SRR26205262	reads/SRR26205262_1.fastq.gz	reads/SRR26205262_2.fastq.gz	assemblies/SRR26205262.fasta	Samonella.yaml
+SRR26205262	reads/SRR26205262_1.fastq.gz	reads/SRR26205262_2.fastq.gz	assemblies/SRR26205262.fasta	Salmonella.yaml
 ERR2929615	reads/ERR2929615_1.fastq.gz	reads/ERR2929615_2.fastq.gz	assemblies/ERR2929615.fasta	E_Faecalis.yaml
 ERR2929578	reads/ERR2929578_1.fastq.gz	reads/ERR2929578_2.fastq.gz	assemblies/ERR2929578.fasta	E_Faecium.yaml
 ERR142064	reads/ERR142064_1.fastq.gz	reads/ERR142064_2.fastq.gz	assemblies/ERR142064.fasta	C_difficile.yaml
diff --git a/src/mmaseq/utils/sample_config.py b/src/mmaseq/utils/sample_config.py
index b452249..2b957f7 100644
--- a/src/mmaseq/utils/sample_config.py
+++ b/src/mmaseq/utils/sample_config.py
@@ -87,9 +87,11 @@ def determine_sample_configs(samplesheet, config_dir, ignore_assemblies):
 
         # Handle missing configuration file
         if not os.path.isfile(cfg_path):
-            print(
-                f"Warning: Config file specified in samplesheet {cfg} "
-                f"does not exist in {config_dir}!"
+            available = sorted(p.name for p in Path(config_dir).glob("*.yaml"))
+            logger.warning(
+                f"Sample '{sample}' references config '{cfg}' which was not "
+                f"found in {config_dir}. Available configs: "
+                f"{', '.join(available) if available else '(none)'}."
             )
             cfg_path = None
 
@@ -97,11 +99,11 @@ def determine_sample_configs(samplesheet, config_dir, ignore_assemblies):
 
             # Ensure that default file exists and use it
             if os.path.exists(default_path):
-                print("Using default.yaml instead")
+                logger.warning(f"Falling back to default.yaml for sample '{sample}'.")
                 cfg_path = default_path
             else:
-                print(
-                    "Warning: Default configuration file is missing, "
+                logger.error(
+                    "Default configuration file is missing, "
                     "please recreate it to enable default analysis: "
                     f"{default_path}"
                 )

From cbe12c7308714864561481e8a598e430c32b68c1 Mon Sep 17 00:00:00 2001
From: SimoneScrima <simonescrima@gmail.com>
Date: Mon, 20 Jul 2026 15:18:00 +0200
Subject: [PATCH 10/13] Added spades to shovill env to avoid crash

---
 src/mmaseq/workflow/envs/shovill.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/mmaseq/workflow/envs/shovill.yaml b/src/mmaseq/workflow/envs/shovill.yaml
index 4bf0530..389f3b8 100644
--- a/src/mmaseq/workflow/envs/shovill.yaml
+++ b/src/mmaseq/workflow/envs/shovill.yaml
@@ -1,3 +1,5 @@
 name: shovill
 dependencies:
+  - bioconda::spades
   - bioconda::shovill
+

From a4a7d45acb8bca43287e9f754e631184357d2875 Mon Sep 17 00:00:00 2001
From: "simonescrima@gmail.com" <simonescrima@gmail.com>
Date: Tue, 21 Jul 2026 12:25:04 +0200
Subject: [PATCH 11/13] Small fix to blastn rule to have a header and wrangle
 better the final output

---
 src/mmaseq/workflow/rules/Analysis.smk | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/mmaseq/workflow/rules/Analysis.smk b/src/mmaseq/workflow/rules/Analysis.smk
index a1f3eff..3534378 100644
--- a/src/mmaseq/workflow/rules/Analysis.smk
+++ b/src/mmaseq/workflow/rules/Analysis.smk
@@ -41,7 +41,11 @@ rule blastn:
         OUTDIR=$(dirname {output.results})
         mkdir -p $OUTDIR
 
-        cmd="blastn -subject {input.database} -query {input.assembly} -outfmt '6' -out {output.results} {params.options}"
+        # Write a header first so the file is self-describing (BLAST outfmt 6 has none),
+        # otherwise the results aggregator consumes the first hit as column names.
+        printf 'qseqid\tsseqid\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore\n' > {output.results}
+
+        cmd="blastn -subject {input.database} -query {input.assembly} -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore' {params.options} >> {output.results}"
 
         echo "Executing command:\n$cmd\n" > {log.stdout} 2>&1
         eval $cmd >> {log.stdout} 2>&1

From 1ad48cc17074992a12fe86d6946b9b831018c6e8 Mon Sep 17 00:00:00 2001
From: "simonescrima@gmail.com" <simonescrima@gmail.com>
Date: Tue, 21 Jul 2026 14:51:18 +0200
Subject: [PATCH 12/13] Fix correct preset for K.oxytoca in kleborate

---
 src/mmaseq/config/species_configs/K_oxytoca.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mmaseq/config/species_configs/K_oxytoca.yaml b/src/mmaseq/config/species_configs/K_oxytoca.yaml
index b9b04b1..8972352 100644
--- a/src/mmaseq/config/species_configs/K_oxytoca.yaml
+++ b/src/mmaseq/config/species_configs/K_oxytoca.yaml
@@ -30,7 +30,7 @@ amrfinder:
     assembler: shovill 
 
 kleborate:
-    options: --preset kpsc
+    options: --preset kosc
     assembler: shovill
 
 mlst:

From c805a318dca7e35650bc07d318f0cf7a0d9dda94 Mon Sep 17 00:00:00 2001
From: Kasper Thystrup Karstensen <kathka@gmail.com>
Date: Mon, 27 Jul 2026 08:58:05 +0200
Subject: [PATCH 13/13] Changed envs for Vanco fetch rules

* Environment for fetching vancomycin and vancomycin_operon changed to py_utils rather than blast for clarity
---
 src/mmaseq/workflow/rules/Databases.smk | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mmaseq/workflow/rules/Databases.smk b/src/mmaseq/workflow/rules/Databases.smk
index ff060d1..07680ce 100644
--- a/src/mmaseq/workflow/rules/Databases.smk
+++ b/src/mmaseq/workflow/rules/Databases.smk
@@ -301,7 +301,7 @@ rule fetch_vancomycin:
     log:
         stdout = f"{logdir}/Databases/fetch_vancomycin.log"
     conda:
-        ENVS_DIR / "blast.yaml"    
+        ENVS_DIR / "py_utls.yaml"
     message:
         "[fetch_vancomycin]: Downloading custom vancomycin database"
     shell:
@@ -325,7 +325,7 @@ rule fetch_vancomycin_operon:
     log:
         stdout = f"{logdir}/Databases/fetch_vancomycin_operon.log"
     conda:
-        ENVS_DIR / "blast.yaml" 
+        ENVS_DIR / "py_utls.yaml"
     message:
         "[fetch_vancomycin_operon]: Downloading custom vancomycin operon database"
     shell: