# HG changeset patch
# User iuc
# Date 1725031196 0
# Node ID 2babe6d5c561f7fa151fe9b3980ad03dba20c997
# Parent  ea8146ee148f04e5777e6c424451f321e24e026e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a

diff -r ea8146ee148f -r 2babe6d5c561 busco.xml
--- a/busco.xml	Mon Mar 18 16:01:49 2024 +0000
+++ b/busco.xml	Fri Aug 30 15:19:56 2024 +0000
@@ -14,7 +14,7 @@
     <version_command>busco --version</version_command>
     <command><![CDATA[
 
-#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
+#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'augustus':
 
 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
@@ -40,8 +40,6 @@
 #if $lineage_conditional.selector == 'cached':
     --offline
     --download_path $lineage_conditional.cached_db.fields.path
-#else
-    --update-data
 #end if
 
 #if $lineage.lineage_mode == "auto_detect":
@@ -50,21 +48,20 @@
     --lineage_dataset '${lineage.lineage_dataset}'
 #end if
 
-#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
-
-    ${busco_mode.use_augustus.long}
-    --augustus
+#if $busco_mode.mode == 'geno':
+    #if $busco_mode.use_augustus.use_augustus_selector == 'miniprot':
+        --miniprot
+    #elif $busco_mode.use_augustus.use_augustus_selector == 'augustus':
+        ${busco_mode.use_augustus.long}
+        --augustus
 
-    #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
-        --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
-    #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
-        --augustus_species local
-    #end if
-#end if
-
-#if str( $busco_mode.mode ) == "geno":
-    #if $busco_mode.miniprot:
-        --miniprot
+        #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
+            --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
+        #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
+            --augustus_species local
+        #end if
+    #else:
+        --metaeuk
     #end if
 #end if
     
@@ -111,14 +108,16 @@
                 <option value="prot">annotated gene sets (protein)</option>
             </param>
             <when value="geno">
-                <param name="miniprot" type="boolean" checked="false" label="Generate miniprot output"/>
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
-                        <option value="yes">Yes, use Augustus</option>
-                        <option value="no" selected="true">Use Metaeuk</option>
+                    <param name="use_augustus_selector" type="select" label="Select a gene predictor" help="In the case of a prokaryotic genome, Prodigal is the default gene predictor">
+                        <option value="augustus">Augustus</option>
+                        <option value="metaeuk">Metaeuk</option>
+                        <option value="miniprot" selected="true">Miniprot</option>
+
                     </param>
-                    <when value="no" />
-                    <when value="yes">
+                    <when value="metaeuk"/>
+                    <when value="miniprot"/>
+                    <when value="augustus">
                         <conditional name="aug_prediction">
                             <param name="augustus_mode" type="select" label="Augustus species model">
                                 <option value="no" selected="true">Use the default species for selected lineage</option>
@@ -189,10 +188,7 @@
         </data>
         <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
             <filter>outputs and 'gff' in outputs</filter>
-        </data>
-        <data name='busco_miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="busco_galaxy/run_*/miniprot_output/*.gff">
-            <filter>busco_mode['mode'] == 'geno' and busco_mode['miniprot']</filter>
-        </data>               
+        </data>              
     </outputs>
     
     <tests>
@@ -205,23 +201,24 @@
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="yes" />
+                    <param name="use_augustus_selector" value="augustus" />
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,missing,gff" />
-            <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" />
-            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
+            <output name="busco_sum">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="Gene predictor used: augustus"/>
+                </assert_contents>
+            </output>
+            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
             <output name="busco_gff">
                 <assert_contents>
                     <has_n_lines n="1"/>
                     <has_text text="##gff-version 3" />
                 </assert_contents>
             </output>
-            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4">
-                <assert_contents>
-                    <has_text text="# BUSCO version is: @TOOL_VERSION@" />
-                </assert_contents>
-            </output>
+            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
         </test>
         <test expect_num_outputs="5">
             <param name="input" value="proteome.fa" />
@@ -233,9 +230,14 @@
                 <param name="mode" value="prot" />
             </conditional>
             <param name="outputs" value="short_summary,missing,image,gff" />
-            <output name="busco_sum" file="proteome_results/short_summary" compare="re_match_multiline" />
-            <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
-            <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
+            <output name="busco_sum">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="BUSCO was run in mode: proteins" />
+                </assert_contents>
+            </output>
+            <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10" />
+            <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10" />
             <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
             <output name="busco_gff">
                 <assert_contents>
@@ -254,13 +256,17 @@
                 <param name="mode" value="tran" />
             </conditional>
             <param name="outputs" value="short_summary,missing,image,gff" />
-            <output name="busco_sum" file="transcriptome_results/short_summary" compare="re_match_multiline" />
+            <output name="busco_sum">
+                <assert_contents>
+                    <has_text text="BUSCO was run in mode: euk_tran" />
+                </assert_contents>
+            </output>
             <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
             <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
             <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
             <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />
         </test>
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="3">
             <param name="input" value="genome.fa" />
             <conditional name="lineage">
                 <param name="lineage_mode" value="select_lineage" />
@@ -268,9 +274,8 @@
             </conditional>
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
-                <param name="miniprot" value="true"/>
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="yes" />
+                    <param name="use_augustus_selector" value="augustus" />
                     <conditional name="aug_prediction">
                         <param name="augustus_mode" value="builtin" />
                         <param name="augustus_species" value="human" />
@@ -278,16 +283,18 @@
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,gff" />
-            <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline"/>
-            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
+            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
+                <assert_contents>
+                    <has_text text="# Gene predictor used: augustus"/>
+                </assert_contents>
+            </output>
+            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
             <output name="busco_gff">
                 <assert_contents>
                     <has_n_lines n="1"/>
                     <has_text text="##gff-version 3" />
                 </assert_contents>
             </output>
-            <!-- The miniprot.gff file is too large. A file containing only the first 1000 lines is used for this test. -->
-            <output name="busco_miniprot" file="genome_results/miniprot_1000.gff" compare="contains" lines_diff="304463"/>
         </test>
         <test expect_num_outputs="3">
             <param name="input" value="genome.fa" />
@@ -298,7 +305,7 @@
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="yes" />
+                    <param name="use_augustus_selector" value="augustus" />
                     <conditional name="aug_prediction">
                         <param name="augustus_mode" value="history" />
                         <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
@@ -306,9 +313,14 @@
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,missing" />
-            <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" />
-            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
-            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
+            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
+                <assert_contents>
+                    <has_text text="# Gene predictor used: augustus"/>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
+            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
+            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10" />
         </test>
         <test expect_num_outputs="5">
             <param name="input" value="genome.fa" />
@@ -319,19 +331,29 @@
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="no" />
+                    <param name="use_augustus_selector" value="metaeuk" />
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,missing,image,gff" />
-            <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="re_match_multiline" />
-            <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />
-            <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />
-            <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
-            <output name="busco_gff" ftype="gff3">
+            <output name="busco_sum">
                 <assert_contents>
-                    <has_n_lines n="13"/>
+                    <has_text text="# Gene predictor used: metaeuk"/>
                 </assert_contents>
             </output>
+            <output name="busco_table" file="genome_results_metaeuk/full_table">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="9647at6656"/>
+                </assert_contents>
+            </output>
+            <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="9647at6656"/>
+                </assert_contents>
+            </output>
+            <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/>
+            <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6" />
         </test>
         <test expect_num_outputs="5">
             <param name="input" value="genome.fa" />
@@ -342,32 +364,49 @@
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="no" />
+                    <param name="use_augustus_selector" value="metaeuk" />
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,missing,image,gff" />
-            <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" />
-            <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="6" />
-            <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" />
+            <output name="busco_sum">
+                <assert_contents>
+                    <has_text text="Gene predictor used: metaeuk"/>
+                </assert_contents>
+            </output>
+            <output name="busco_table">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="The lineage dataset is: eukaryota_odb10"/>
+                </assert_contents>
+            </output>
+            <output name="busco_missing">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="The lineage dataset is: eukaryota_odb10"/>
+                </assert_contents>
+            </output>
             <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
             <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="input" value="genome.fa" />
-            <conditional name="lineage_conditional">
-                <param name="selector" value="cached"/>
-                <param name="cached_db" value="busco-demo-db-20230328"/>
-            </conditional>
             <conditional name="lineage">
                 <param name="lineage_mode" value="select_lineage" />
-                <param name="lineage_dataset" value="archaea_odb10" />
+                <param name="lineage_dataset" value="arthropoda_odb10" />
             </conditional>
-            <param name="outputs" value="short_summary" />
-            <output name="busco_sum" file="genome_results/short_summary_cached" compare="diff" lines_diff="6" />
-            <output name="busco_table" file="genome_results/full_table_cached" compare="diff" lines_diff="4" />
-            <assert_stdout>
-                <has_text text="Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)"/>
-            </assert_stdout>
+            <param name="outputs" value="short_summary,gff" />
+            <output name="busco_sum">
+                <assert_contents>
+                    <has_text text="# Gene predictor used: miniprot"/>
+                </assert_contents>
+            </output>
+            <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff" />
+            <output name="busco_table" file="genome_results_miniprot/full_table">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="9647at6656"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
diff -r ea8146ee148f -r 2babe6d5c561 macros.xml
--- a/macros.xml	Mon Mar 18 16:01:49 2024 +0000
+++ b/macros.xml	Fri Aug 30 15:19:56 2024 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">5.5.0</token>
+    <token name="@TOOL_VERSION@">5.7.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="citations">
diff -r ea8146ee148f -r 2babe6d5c561 test-data/busco_database.loc
--- a/test-data/busco_database.loc	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/busco_database.loc	Fri Aug 30 15:19:56 2024 +0000
@@ -3,4 +3,4 @@
 # - name
 # - version
 # - /path/to/data 
-busco-demo-db-20230328	BUSCO-DEMO-DB-20230328	5.4.6	${__HERE__}/test-db/busco_downloads
+busco-demo-db-20230328	BUSCO-DEMO-DB-20230328	5.4.6	${__HERE__}/test-db/busco_downloads
\ No newline at end of file
diff -r ea8146ee148f -r 2babe6d5c561 test-data/busco_downloads/file_versions.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/busco_downloads/file_versions.tsv	Fri Aug 30 15:19:56 2024 +0000
@@ -0,0 +1,213 @@
+acidobacteria_odb10	2024-01-08	13046d110cf6d038af269ee6e0681bdc	Prokaryota	lineages
+aconoidasida_odb10	2024-01-08	47b6ece13859b681466c79f4e6c6d1ad	Eukaryota	lineages
+actinobacteria_class_odb10	2024-01-08	0a326071854e20d1977a13a5e3a5f84f	Prokaryota	lineages
+actinobacteria_phylum_odb10	2024-01-08	eaa25a3d973f580d4cf59b7251309e5a	Prokaryota	lineages
+actinopterygii_odb10	2024-01-08	6b042870822559fcacf129fdedea8927	Eukaryota	lineages
+agaricales_odb10	2024-01-08	1bf1c632dab6ae5b4ff0be6fad8ff8cf	Eukaryota	lineages
+agaricomycetes_odb10	2024-01-08	717f3e2543617972c9a45bbd4ac975b6	Eukaryota	lineages
+alphaproteobacteria_odb10	2024-01-08	22db70ba9f321e8b8f4eed0b2be41b6f	Prokaryota	lineages
+alteromonadales_odb10	2024-01-08	0a959f97971c349fdd69bc37e7796514	Prokaryota	lineages
+alveolata_odb10	2024-01-08	cbd2ddb6b18efb2b4ca218a74688aacf	Eukaryota	lineages
+apicomplexa_odb10	2024-01-08	e27eb839243c4a4280e4187108b48596	Eukaryota	lineages
+aquificae_odb10	2024-01-08	0285bccb18097979aef7badd2b554378	Prokaryota	lineages
+arachnida_odb10	2024-01-08	625818d0544cd760356af0b8e9a5a412	Eukaryota	lineages
+archaea_odb10	2024-01-08	3eb26c670c520c0f3b32bff46fce03d7	Prokaryota	lineages
+arthropoda_odb10	2024-01-08	915ae2790da249b81eceeb1cea2ad922	Eukaryota	lineages
+ascomycota_odb10	2024-01-08	694c2ad193a01cd6e95487a3ddcbcce8	Eukaryota	lineages
+aves_odb10	2024-01-08	eea0b7e8122b1f528c97c142e9ddfd82	Eukaryota	lineages
+bacillales_odb10	2024-01-08	e2fb5d46b90c76f849d9ec9c49ae79ca	Prokaryota	lineages
+bacilli_odb10	2024-01-08	e8dc4ad8c6e26e2dfc47e155736896bd	Prokaryota	lineages
+bacteria_odb10	2024-01-08	bff9523df89980699c01e8f31e490496	Prokaryota	lineages
+bacteroidales_odb10	2024-01-08	60e4d09d2526ad90561bc0ad4c67f783	Prokaryota	lineages
+bacteroidetes-chlorobi_group_odb10	2024-01-08	4d2ae5165b8aec5f42f42d79e98bc05d	Prokaryota	lineages
+bacteroidetes_odb10	2024-01-08	81eddd495a27b2c15b661eb2f018b01b	Prokaryota	lineages
+bacteroidia_odb10	2024-01-08	1756db675bfee79e3a3a6e9946003038	Prokaryota	lineages
+basidiomycota_odb10	2024-01-08	55ee0a0b2ca18812393fd43faf4f1897	Eukaryota	lineages
+betaproteobacteria_odb10	2024-01-08	040cf23dfcfc0fa632bd48fde213b61f	Prokaryota	lineages
+boletales_odb10	2024-01-08	7a7b1635d171d069a5525ee24faf8c83	Eukaryota	lineages
+brassicales_odb10	2024-01-08	7f96488b36e2f391dd594a099b31ea24	Eukaryota	lineages
+burkholderiales_odb10	2024-01-08	b41288c7ab665a79a592214850af3dcf	Prokaryota	lineages
+campylobacterales_odb10	2024-01-08	950fa5f90829dfbfe879e71f22d8a6f1	Prokaryota	lineages
+capnodiales_odb10	2024-01-08	a1601671360646aa38c968520f81a9bc	Eukaryota	lineages
+carnivora_odb10	2024-01-08	a81b85b7d90b046315b8cb1bea8605c1	Eukaryota	lineages
+cellvibrionales_odb10	2024-01-08	4284a714433698dfcf38b7297bc6ef4b	Prokaryota	lineages
+cetartiodactyla_odb10	2024-01-08	7d348bed34a92a77c86adb4194a4d0cc	Eukaryota	lineages
+chaetothyriales_odb10	2024-01-08	721a498d4da22ab75c48a705cb7ffafe	Eukaryota	lineages
+chlamydiae_odb10	2024-01-08	f9a0d5d18b525f5b25ffd28cbc79511a	Prokaryota	lineages
+chlorobi_odb10	2024-01-08	1accab3fc927c6e614d96d3b76eb7d41	Prokaryota	lineages
+chloroflexi_odb10	2024-01-08	9633d49879fba7efe9d59e9ec1f6fb70	Prokaryota	lineages
+chlorophyta_odb10	2024-01-08	7dbcc25dd421be9fbb0f0ae0d7095284	Eukaryota	lineages
+chromatiales_odb10	2024-01-08	113389b263ee38c451831b513a56ae85	Prokaryota	lineages
+chroococcales_odb10	2024-01-08	319aa6d9e5ce2606aecfc0bce4419eb8	Prokaryota	lineages
+clostridiales_odb10	2024-01-08	9b90a303dc2395f6197c1d64f03fbfc0	Prokaryota	lineages
+clostridia_odb10	2024-01-08	7eeb8a01b7c4643aa9fbbd1fd03c887f	Prokaryota	lineages
+coccidia_odb10	2024-01-08	ec804a941baabf38053a0f8b8c7021dd	Eukaryota	lineages
+coriobacteriales_odb10	2024-01-08	18776c9d1cf45a170a71a57e6b0bf32c	Prokaryota	lineages
+coriobacteriia_odb10	2024-01-08	6837d15f63527b8b9ad624f9e4a26daf	Prokaryota	lineages
+corynebacteriales_odb10	2024-01-08	af866d8ea389f71092f9344fb9603f5c	Prokaryota	lineages
+cyanobacteria_odb10	2024-01-08	26b249d637a4146011f38bcf70c6d6f3	Prokaryota	lineages
+cyprinodontiformes_odb10	2024-01-08	4f85a35eafec1392512eba8b6011dfce	Eukaryota	lineages
+cytophagales_odb10	2024-01-08	6ec59af7cc8d6f6d5de4c6f22f5eb5f0	Prokaryota	lineages
+cytophagia_odb10	2024-01-08	ccecc5c2a542cf3d75330c1eacbd3100	Prokaryota	lineages
+delta-epsilon-subdivisions_odb10	2024-01-08	911bdaa6c96bef4feaadd29846681cbd	Prokaryota	lineages
+deltaproteobacteria_odb10	2024-01-08	93caf5a115cffaf8089f47b7e592024a	Prokaryota	lineages
+desulfobacterales_odb10	2024-01-08	6a47df2907b67b809b29291ad9baadeb	Prokaryota	lineages
+desulfovibrionales_odb10	2024-01-08	2e4e5bc1e1e38533273013a92d59e6f8	Prokaryota	lineages
+desulfurococcales_odb10	2024-01-08	74cc4abc7ed82901712888c2408fb667	Prokaryota	lineages
+desulfuromonadales_odb10	2024-01-08	b6aad868c8158fc9f92f7c7969e6bd65	Prokaryota	lineages
+diptera_odb10	2024-01-08	da520a013d41c04d92a4b18b59803628	Eukaryota	lineages
+dothideomycetes_odb10	2024-01-08	f3b8e2745f0d1cca41d9d4c171b1e70e	Eukaryota	lineages
+embryophyta_odb10	2024-01-08	7d4e9894b0727223f8ef24cf05b7a71d	Eukaryota	lineages
+endopterygota_odb10	2024-01-08	fd7f8c8e521f96c0d273c1b25ef262ea	Eukaryota	lineages
+enterobacterales_odb10	2024-01-08	989af5b1fe5e6b7ff7692511a412c1f6	Prokaryota	lineages
+entomoplasmatales_odb10	2024-01-08	65893ded2df1ffc7bf4cc8abce3a858a	Prokaryota	lineages
+epsilonproteobacteria_odb10	2024-01-08	b0eaa68282aab72d8a2447da767219da	Prokaryota	lineages
+euarchontoglires_odb10	2024-01-08	4f6b07a49e990f1a821db285f808f7a7	Eukaryota	lineages
+eudicots_odb10	2024-01-08	38ece5baf0523143fc6594030bca4487	Eukaryota	lineages
+euglenozoa_odb10	2024-01-08	2422e36739d888b5400211e128442e6f	Eukaryota	lineages
+eukaryota_odb10	2024-01-08	93e2a6ec05708dbf0f23db078b88c5a8	Eukaryota	lineages
+eurotiales_odb10	2024-01-08	476a061e592590139598c5ed610d1883	Eukaryota	lineages
+eurotiomycetes_odb10	2024-01-08	077c5b9805d1bd69772851e7a3ef7e2f	Eukaryota	lineages
+euryarchaeota_odb10	2024-01-08	152262b6845431b05feb15919745af78	Prokaryota	lineages
+eutheria_odb10	2024-01-08	2a3b171b152e781d8b905fb1861b701a	Eukaryota	lineages
+fabales_odb10	2024-01-08	b830d5061c0edd67d49a69800ac58598	Eukaryota	lineages
+firmicutes_odb10	2024-01-08	4610a6bc81861850b4d8fc3b33fa7a5c	Prokaryota	lineages
+flavobacteriales_odb10	2024-01-08	d8514f1c520e2fe1f3c7d36906f895c4	Prokaryota	lineages
+flavobacteriia_odb10	2024-01-08	d4bead34b6d89f0a3e36b5250941726d	Prokaryota	lineages
+fungi_odb10	2024-01-08	d389cb627ded374b47db05630191494e	Eukaryota	lineages
+fusobacteriales_odb10	2024-01-08	c25c6d2e434d2ad8f91f6d5bccce30a5	Prokaryota	lineages
+fusobacteria_odb10	2024-01-08	4e249141ccd9f730e52d386f2b9c0185	Prokaryota	lineages
+gammaproteobacteria_odb10	2024-01-08	5ade21bee041306a5a12a4c2047d978d	Prokaryota	lineages
+glires_odb10	2024-01-08	e556d8cd17fc9ed1ee6ffd1275809268	Eukaryota	lineages
+glomerellales_odb10	2024-01-08	d1de6bb04a0d4ed8c816dbb62586faff	Eukaryota	lineages
+halobacteriales_odb10	2024-01-08	79b455d2fe7a132673d7e40a3d123370	Prokaryota	lineages
+halobacteria_odb10	2024-01-08	0b1efa4df56adb7423df34505c1c7814	Prokaryota	lineages
+haloferacales_odb10	2024-01-08	99e1945897e61256586c478dd8678cdc	Prokaryota	lineages
+helotiales_odb10	2024-01-08	68b7b6ae8f5f933a282000711e163a3a	Eukaryota	lineages
+hemiptera_odb10	2024-01-08	02bc28602cd3ec17f3b3bda43e3a2888	Eukaryota	lineages
+hymenoptera_odb10	2024-01-08	9d10047e5500f51c48104c9784baf6e5	Eukaryota	lineages
+hypocreales_odb10	2024-01-08	2f85af3da8d3e9b20daf47c924ad4385	Eukaryota	lineages
+insecta_odb10	2024-01-08	fe5d4360ef9829c3c663acab4fe1f1da	Eukaryota	lineages
+lactobacillales_odb10	2024-01-08	1377e13f55575410373f78d984e6d49b	Prokaryota	lineages
+laurasiatheria_odb10	2024-01-08	4b69d3754077ee8a121ff4c1a814038b	Eukaryota	lineages
+legionellales_odb10	2024-01-08	0432b6cbcce14bcf292ae8fd01202f81	Prokaryota	lineages
+leotiomycetes_odb10	2024-01-08	7c6ef2d12e2c7529097ac033b46f43df	Eukaryota	lineages
+lepidoptera_odb10	2024-01-08	4ad4f7c458c170c0b3245712b4e1cf1e	Eukaryota	lineages
+liliopsida_odb10	2024-01-08	154552d116896e02c282a7d91791cb7d	Eukaryota	lineages
+lineages_list.txt	2021-12-14	ebe3d982a830281588e287cf72f3b5e1	NaN	information
+list_of_reference_markers.archaea_odb10.txt	2019-12-16	0143477e3666a5bcdec26a826eb01ab4	Prokaryota	placement_files
+list_of_reference_markers.bacteria_odb10.txt	2019-12-16	e82a39f3060123f4322057c632d7691c	Prokaryota	placement_files
+list_of_reference_markers.eukaryota_odb10.txt	2019-12-16	95a02d2bbe1659778bda594d59c90ee1	Eukaryota	placement_files
+mammalia_odb10	2024-01-08	5e1b55c306640771a7700d36ae67e1e2	Eukaryota	lineages
+mapping_taxid-lineage.archaea_odb10.txt	2019-12-16	5a05ab8eb491f6d4ae9f7774fd778f7e	Prokaryota	placement_files
+mapping_taxid-lineage.bacteria_odb10.txt	2019-12-16	b25a5a807f4ff70f4343ef7500d26975	Prokaryota	placement_files
+mapping_taxid-lineage.eukaryota_odb10.txt	2019-12-16	e5b047a09cee36f1116f7de1453276b4	Eukaryota	placement_files
+mapping_taxids-busco_dataset_name.archaea_odb10.txt	2019-12-16	d8cc75b75e052e475e07d84cb4d8cd06	Prokaryota	placement_files
+mapping_taxids-busco_dataset_name.bacteria_odb10.txt	2019-12-16	79514724345b6cae32bb05ecacc11386	Prokaryota	placement_files
+mapping_taxids-busco_dataset_name.eukaryota_odb10.txt	2019-12-16	435492f974732bb2d562d5abe54bd494	Eukaryota	placement_files
+metazoa_odb10	2024-01-08	3372747bddabccabfdc291fcd4114899	Eukaryota	lineages
+methanobacteria_odb10	2024-01-08	36df24c0adf12f76fbd7d26ce417b2c1	Prokaryota	lineages
+methanococcales_odb10	2024-01-08	bfb1b8d0781c6d55bc89fa4fd84f5a1d	Prokaryota	lineages
+methanomicrobiales_odb10	2024-01-08	4b210069ed2c656fd1f60b55d35a70ad	Prokaryota	lineages
+methanomicrobia_odb10	2024-01-08	2e63c7dfddb70829fd1d3ed87d30611f	Prokaryota	lineages
+micrococcales_odb10	2024-01-08	fdb78019a92964e96b4745defaafc1c4	Prokaryota	lineages
+microsporidia_odb10	2024-01-08	c6c96c9fddc451b403ba83630506101e	Eukaryota	lineages
+mollicutes_odb10	2024-01-08	893e2e596fe937d72b92b81700d5b3e4	Prokaryota	lineages
+mollusca_odb10	2024-01-08	d35dfcd38630fb8cb15c646c2482835b	Eukaryota	lineages
+mucorales_odb10	2024-01-08	3cc5cf5b74b429aad5d62704a041c355	Eukaryota	lineages
+mucoromycota_odb10	2024-01-08	4210498ca504de64e5c9818c8f64962a	Eukaryota	lineages
+mycoplasmatales_odb10	2024-01-08	36cd7fda07a206d9db3ce0c97cdc0025	Prokaryota	lineages
+natrialbales_odb10	2024-01-08	efa92043b2440ada26425919f875349a	Prokaryota	lineages
+neisseriales_odb10	2024-01-08	b829a1f5314ebf1f949af4f0e28de0e2	Prokaryota	lineages
+nematoda_odb10	2024-01-08	ec87bb045e2a81868518b1071029d759	Eukaryota	lineages
+nitrosomonadales_odb10	2024-01-08	5877c85915cbb39a3cf66c9b8c296cf8	Prokaryota	lineages
+nostocales_odb10	2024-01-08	2564ddc82836e0d1164d8ab43a78b68a	Prokaryota	lineages
+oceanospirillales_odb10	2024-01-08	68600b75c362f9fe8ff2811d141e9cc0	Prokaryota	lineages
+onygenales_odb10	2024-01-08	6e6b4e1334bb077295ae799c20b38c85	Eukaryota	lineages
+oscillatoriales_odb10	2024-01-08	58987c4c5fff2c82d473a26c40c6b661	Prokaryota	lineages
+passeriformes_odb10	2024-01-08	41e0a9cbc2c93aa4fd5cd3e8c2876b56	Eukaryota	lineages
+pasteurellales_odb10	2024-01-08	d9d0d1500ddc1c79f705ea58d233aff8	Prokaryota	lineages
+planctomycetes_odb10	2024-01-08	4779117e2b4f688e2bdf84faa5806294	Prokaryota	lineages
+plasmodium_odb10	2024-01-08	dcc21aada8d28ab5caf7db5b13b19db6	Eukaryota	lineages
+pleosporales_odb10	2024-01-08	724410708694d64cabc152f5d343a48b	Eukaryota	lineages
+poales_odb10	2024-01-08	e816664c71d968404b2e0acc49d18a44	Eukaryota	lineages
+polyporales_odb10	2024-01-08	27e685efdb0e3abe27c1b7635a07360d	Eukaryota	lineages
+primates_odb10	2024-01-08	321262a9dd0dcb01b92680e90ec6f344	Eukaryota	lineages
+propionibacteriales_odb10	2024-01-08	ec081179e55c395689bb9099dedeceb7	Prokaryota	lineages
+proteobacteria_odb10	2024-01-08	6bb05a7389ee093cbd2bf9261ea4c608	Prokaryota	lineages
+pseudomonadales_odb10	2024-01-08	b966b8bb3e542085dd4337ef5e692f83	Prokaryota	lineages
+rhizobiales_odb10	2024-01-08	17f8d1d055dc8f4ff121cad29a86f200	Prokaryota	lineages
+rhizobium-agrobacterium_group_odb10	2024-01-08	6bcf42ae66ea48608394b737d54cecfb	Prokaryota	lineages
+rhodobacterales_odb10	2024-01-08	95a00f9c488274d5eb2d00f20485741b	Prokaryota	lineages
+rhodospirillales_odb10	2024-01-08	0890d70c48d570c36a09abea2575cc6a	Prokaryota	lineages
+rickettsiales_odb10	2024-01-08	3a3c78aa761117f38cb9a43cd3fd3f64	Prokaryota	lineages
+saccharomycetes_odb10	2024-01-08	8b6e1a7e088592717f9677fdf15da697	Eukaryota	lineages
+sauropsida_odb10	2024-01-08	9cc70aa59593e937612bef7c27d1edaf	Eukaryota	lineages
+selenomonadales_odb10	2024-01-08	56c4bd6baa137ddd0d83f9c924261ec4	Prokaryota	lineages
+solanales_odb10	2024-01-08	66f358ec9289490e465b49c534d68963	Eukaryota	lineages
+sordariomycetes_odb10	2024-01-08	d2eaf7b7dcdc98c696193200a64f680b	Eukaryota	lineages
+sphingobacteriia_odb10	2024-01-08	242603fe2ff0935de82a73610d3c7ecf	Prokaryota	lineages
+sphingomonadales_odb10	2024-01-08	0d2a778d7223204d457fed9159c3cd0b	Prokaryota	lineages
+spirochaetales_odb10	2024-01-08	25566c0ec1f4157549b29909987fe2dc	Prokaryota	lineages
+spirochaetes_odb10	2024-01-08	791cb6d5240aee08cbfc31aa46c95fea	Prokaryota	lineages
+spirochaetia_odb10	2024-01-08	2d872abdb7804ed46d064ebf1a4af183	Prokaryota	lineages
+stramenopiles_odb10	2024-01-08	c47e74b9b44f96393aab60a94da41d9b	Eukaryota	lineages
+streptomycetales_odb10	2024-01-08	0fa3b1d4ad18d32f22cfa3e9df6c5f24	Prokaryota	lineages
+streptosporangiales_odb10	2024-01-08	efc360354567844fa58da793f464eb81	Prokaryota	lineages
+sulfolobales_odb10	2024-01-08	8a61f401552651f1a65901602ebeafe8	Prokaryota	lineages
+supermatrix.aln.archaea_odb10.faa	2019-12-16	e9d2c8065a7779f9447b154b9030bcf8	Prokaryota	placement_files
+supermatrix.aln.bacteria_odb10.faa	2019-12-16	eba6a090cbe21abe1db69d841e8231bc	Prokaryota	placement_files
+supermatrix.aln.eukaryota_odb10.faa	2019-12-16	3584e9fb12211b8c8c3ad63666444be1	Eukaryota	placement_files
+synechococcales_odb10	2024-01-08	9a472bbb3c02e033f3672644bbb27779	Prokaryota	lineages
+synergistetes_odb10	2024-01-08	a5bf4d9973e8ea1fbdf3ea8284bd8957	Prokaryota	lineages
+tenericutes_odb10	2024-01-08	f2bbba733d5b3a531ba14d7338d2fb8f	Prokaryota	lineages
+tetrapoda_odb10	2024-01-08	536277f71a4369b266c77c46d7e4fc1b	Eukaryota	lineages
+thaumarchaeota_odb10	2024-01-08	216d7dfaa4b307e5bf6f136bf310cece	Prokaryota	lineages
+thermoanaerobacterales_odb10	2024-01-08	d66c7a944c1f36dc22353a62e663065b	Prokaryota	lineages
+thermoplasmata_odb10	2024-01-08	f3ec5b6d8fa79c4c6caa37e6b0c09776	Prokaryota	lineages
+thermoproteales_odb10	2024-01-08	c92700b9bc1018ba50741c453632a758	Prokaryota	lineages
+thermoprotei_odb10	2024-01-08	e9c08ac322b0c8e4d1c052e6738ad85d	Prokaryota	lineages
+thermotogae_odb10	2024-01-08	546306dabbd386be2d9940a2c0d0deb1	Prokaryota	lineages
+thiotrichales_odb10	2024-01-08	7871f11be31cf3dfb0f57e8a1f5b31f1	Prokaryota	lineages
+tissierellales_odb10	2024-01-08	d5651b1b2e07433fc212881bd1482b72	Prokaryota	lineages
+tissierellia_odb10	2024-01-08	f56b85fda5d5cb55322a8cbd452dd365	Prokaryota	lineages
+tree.archaea_odb10.nwk	2019-12-16	23a9602460ca3ba12a4382964c40add4	Prokaryota	placement_files
+tree.bacteria_odb10.nwk	2019-12-16	3cbe2d6292e02ee78b92b42ec7c13bf5	Prokaryota	placement_files
+tree.eukaryota_odb10.nwk	2019-12-16	cb0d434ee9d87f5d6babd1832a3fa419	Eukaryota	placement_files
+tree_metadata.archaea_odb10.txt	2019-12-16	1cc8a1284c883d9a5a8e33e70a81a743	Prokaryota	placement_files
+tree_metadata.bacteria_odb10.txt	2019-12-16	04a34d1dbcc0814bd0f5acee1d2a9c3f	Prokaryota	placement_files
+tree_metadata.eukaryota_odb10.txt	2019-12-16	589ac2a41cb79863d4b0b061e472afea	Eukaryota	placement_files
+tremellomycetes_odb10	2024-01-08	a0bfe1ffe4313753173cd341ddcc4c07	Eukaryota	lineages
+verrucomicrobia_odb10	2024-01-08	1c380e10eaac2482a9485fe14b7bad47	Prokaryota	lineages
+vertebrata_odb10	2024-01-08	d292737afaec0ac95bde4f4a8d2ea814	Eukaryota	lineages
+vibrionales_odb10	2024-01-08	e9ec5827bed867a01d07d7d03aaddc4c	Prokaryota	lineages
+viridiplantae_odb10	2024-01-08	90d6ce27fde83f1e4aba1d6a8f523673	Eukaryota	lineages
+xanthomonadales_odb10	2024-01-08	47dd98a24916b28b52500e9a036eb8a8	Prokaryota	lineages
+alphaherpesvirinae_odb10	2024-01-08	44433a26b31aa50e4314a013eb2d1ff4	Virus	lineages
+baculoviridae_odb10	2024-01-08	78a612f186cb5b88ec8c030661e46487	Virus	lineages
+rudiviridae_odb10	2024-01-08	afad43502a74667304b97a39459700b4	Virus	lineages
+betaherpesvirinae_odb10	2024-01-08	1fd9d15097a377d712c6458451bf65af	Virus	lineages
+herpesviridae_odb10	2024-01-08	79856510300f9379e518cc8180ad14fb	Virus	lineages
+poxviridae_odb10	2024-01-08	4cb2e71a92b2088a0a0b1f4ff20f94ef	Virus	lineages
+tevenvirinae_odb10	2024-01-08	fac34fac2c70199fcbe69c0a7a663d71	Virus	lineages
+aviadenovirus_odb10	2024-01-08	f9c946051627e87ff717ad466d6c5966	Virus	lineages
+enquatrovirus_odb10	2024-01-08	f6c05f3de730a09cc7eaf58bcc50636c	Virus	lineages
+teseptimavirus_odb10	2024-01-08	18d63d8e679c6fc6086d906d6b917f05	Virus	lineages
+bclasvirinae_odb10	2024-01-08	51a9dce485c577e575d411d10c566820	Virus	lineages
+fromanvirus_odb10	2024-01-08	48f5b7b57afa387315c9e006410f55b9	Virus	lineages
+skunavirus_odb10	2024-01-08	68fbb8404853ae930651c3af1baa7b49	Virus	lineages
+betabaculovirus_odb10	2024-01-08	aab73c1e308f8a1cec4f4529b06ee3d4	Virus	lineages
+pahexavirus_odb10	2024-01-08	3b1410a4b594471e05c0b4d466e3173b	Virus	lineages
+alphabaculovirus_odb10	2024-01-08	ec04ed01eab6001f35c1a6ebfc70180f	Virus	lineages
+tunavirinae_odb10	2024-01-08	fe8a69addddcbc43732a4504aff538e2	Virus	lineages
+simplexvirus_odb10	2024-01-08	fffd2907f63fe04c78fabd61d2f56919	Virus	lineages
+gammaherpesvirinae_odb10	2024-01-08	da764ed072f3fb78cae2ff7e90868a9f	Virus	lineages
+varicellovirus_odb10	2024-01-08	43c79da0fb65e9d5941d71458cf844ad	Virus	lineages
+cheoctovirus_odb10	2024-01-08	74dacf2a763c2a462356ded5e79921db	Virus	lineages
+guernseyvirinae_odb10	2024-01-08	484f59b9efc120c118fae2e6c178ffaa	Virus	lineages
+tequatrovirus_odb10	2024-01-08	67a3c9d25ded118212840dfd87c37d96	Virus	lineages
+chordopoxvirinae_odb10	2024-01-08	c5ff51b8e86771a94400c0df8f8eb383	Virus	lineages
+peduovirus_odb10	2024-01-08	660b6c8dae78bf76bddd9ba1be2c8bd9	Virus	lineages
+iridoviridae_odb10	2024-01-08	3b3e67bb85d616fd874b26479d6abaea	Virus	lineages
+spounavirinae_odb10	2024-01-08	286365f43fe02aad53b89555d36cd6b0	Virus	lineages
+virus_datasets.txt	2020-11-26	a7d1e4d4bb6327d01efde3bcc8658cb3	NaN	information
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results/full_table
--- a/test-data/genome_results/full_table	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/genome_results/full_table	Fri Aug 30 15:19:56 2024 +0000
@@ -1,5 +1,5 @@
-# BUSCO version is: 5.5.0 
-# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
 774at6656	Missing
 980at6656	Missing
@@ -509,7 +509,7 @@
 93535at6656	Missing
 93797at6656	Missing
 94054at6656	Missing
-94238at6656	Complete	sample:34764-38486	34764	38486	-	60.7	116	https://www.orthodb.org/v10?query=94238at6656	checkpoint protein HUS1
+94238at6656	Complete	sample	38486	34764	-	60.7	116	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
 94263at6656	Missing
 94304at6656	Missing
 94473at6656	Missing
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results/full_table_cached
--- a/test-data/genome_results/full_table_cached	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/genome_results/full_table_cached	Fri Aug 30 15:19:56 2024 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.5.0 
+# BUSCO version is: 5.7.1 
 # The lineage dataset is: archaea_odb10 (Creation date: 2021-02-23, number of genomes: 404, number of BUSCOs: 194)
 # Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length
 860at2157	Missing
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results/missing_buscos_list
--- a/test-data/genome_results/missing_buscos_list	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/genome_results/missing_buscos_list	Fri Aug 30 15:19:56 2024 +0000
@@ -1,5 +1,5 @@
-# BUSCO version is: 5.5.0 
-# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
 100136at6656
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results/short_summary
--- a/test-data/genome_results/short_summary	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/genome_results/short_summary	Fri Aug 30 15:19:56 2024 +0000
@@ -1,35 +1,36 @@
-# BUSCO version is: 5\.5\.0 
-# The lineage dataset is: arthropoda_odb10 \(Creation date: [0-9]{4}-[0-9]{2}-[0-9]{2}, number of genomes: 90, number of BUSCOs: 1013\)
-# Summarized benchmarking in BUSCO notation for file [a-z0-9_\-/\.]+
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
+# Summarized benchmarking in BUSCO notation for file /tmp/tmpl5l1blpe/files/7/a/3/dataset_7a33f452-1064-4b4a-943f-b0efef6a4a4a.dat
 # BUSCO was run in mode: euk_genome_aug
 # Gene predictor used: augustus
 
-	\*\*\*\*\* Results: \*\*\*\*\*
+	***** Results: *****
 
-	C:0\.1%\[S:0\.1%,D:0\.0%\],F:0\.0%,M:99\.9%,n:1013	   
-	1	Complete BUSCOs \(C\)			   
-	1	Complete and single-copy BUSCOs \(S\)	   
-	0	Complete and duplicated BUSCOs \(D\)	   
-	0	Fragmented BUSCOs \(F\)			   
-	1012	Missing BUSCOs \(M\)			   
+	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013	   
+	1	Complete BUSCOs (C)			   
+	1	Complete and single-copy BUSCOs (S)	   
+	0	Complete and duplicated BUSCOs (D)	   
+	0	Fragmented BUSCOs (F)			   
+	1012	Missing BUSCOs (M)			   
 	1013	Total BUSCO groups searched		   
 
 Assembly Statistics:
 	1	Number of scaffolds
 	1	Number of contigs
 	62370	Total length
-	0\.000%	Percent gaps
+	0.000%	Percent gaps
 	62 KB	Scaffold N50
 	62 KB	Contigs N50
 
 
 Dependencies and versions:
-	hmmsearch: [0-9\.\+]+
-	bbtools: [0-9\.\+]+
-	makeblastdb: [0-9\.\+]+
-	tblastn: [0-9\.\+]+
-	augustus: [0-9\.\+]+
-	gff2gbSmallDNA\.pl: None
-	new_species\.pl: None
+	hmmsearch: 3.1
+	bbtools: 39.06
+	makeblastdb: 2.15.0+
+	tblastn: 2.15.0+
+	augustus: 3.5.0
+	gff2gbSmallDNA.pl: None
+	new_species.pl: None
 	etraining: None
-	busco: [0-9\.\+]+
+	python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0)
+	busco: 5.7.1
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results/short_summary_cached
--- a/test-data/genome_results/short_summary_cached	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/genome_results/short_summary_cached	Fri Aug 30 15:19:56 2024 +0000
@@ -1,7 +1,7 @@
-# BUSCO version is: 5.5.0 
+# BUSCO version is: 5.7.1 
 # The lineage dataset is: archaea_odb10 (Creation date: 2021-02-23, number of genomes: 404, number of BUSCOs: 194)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmpbmq1q2c6/files/3/3/0/dataset_330f49ed-7a6b-4380-870f-22494bb4b257.dat
-# BUSCO was run in mode: prok_genome
+# Summarized benchmarking in BUSCO notation for file /tmp/tmprlx1s52v/files/e/8/d/dataset_e8d136af-46c1-4ffa-abaf-e8899526d2b0.dat
+# BUSCO was run in mode: prok_genome_prod
 # Gene predictor used: prodigal
 
 	***** Results: *****
@@ -27,4 +27,5 @@
 	hmmsearch: 3.1
 	bbtools: 39.01
 	prodigal: 2.6.3
-	busco: 5.5.0
+	python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0)
+	busco: 5.7.1
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk/full_table
--- a/test-data/genome_results_metaeuk/full_table	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/genome_results_metaeuk/full_table	Fri Aug 30 15:19:56 2024 +0000
@@ -1,5 +1,5 @@
-# BUSCO version is: 5.5.0 
-# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
 774at6656	Missing
 980at6656	Missing
@@ -340,7 +340,7 @@
 68939at6656	Missing
 68961at6656	Missing
 68981at6656	Missing
-68987at6656	Complete	sample:40255-42070	40255	42070	+	122.8	266	https://www.orthodb.org/v10?query=68987at6656	mannose-1-phosphate guanyltransferase alpha
+68987at6656	Complete	sample	40255	42070	+	122.8	266	https://v10-1.orthodb.org/?query=68987at6656	Nucleotidyl transferase domain
 69201at6656	Missing
 69238at6656	Missing
 69284at6656	Missing
@@ -509,7 +509,7 @@
 93535at6656	Missing
 93797at6656	Missing
 94054at6656	Missing
-94238at6656	Complete	sample:35678-34845	34845	35678	-	60.7	116	https://www.orthodb.org/v10?query=94238at6656	checkpoint protein HUS1
+94238at6656	Complete	sample	35693	34845	-	60.6	116	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
 94263at6656	Missing
 94304at6656	Missing
 94473at6656	Missing
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk/missing_buscos_list
--- a/test-data/genome_results_metaeuk/missing_buscos_list	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/genome_results_metaeuk/missing_buscos_list	Fri Aug 30 15:19:56 2024 +0000
@@ -1,5 +1,5 @@
-# BUSCO version is: 5.5.0 
-# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
 100136at6656
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk/out.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results_metaeuk/out.gff3	Fri Aug 30 15:19:56 2024 +0000
@@ -0,0 +1,3 @@
+##gff-version 3
+sample	MetaEuk	gene	40256	42071	198	+	.	Target_ID=68987at6656_29053_0:00071c;TCS_ID=68987at6656_29053_0:00071c|sample|+|40255
+sample	MetaEuk	gene	34846	35694	527	-	.	Target_ID=94238at6656_7245_0:00200b;TCS_ID=94238at6656_7245_0:00200b|sample|-|34845
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk/short_summary
--- a/test-data/genome_results_metaeuk/short_summary	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/genome_results_metaeuk/short_summary	Fri Aug 30 15:19:56 2024 +0000
@@ -1,30 +1,32 @@
-# BUSCO version is: 5\.5\.0 
-# The lineage dataset is: arthropoda_odb10 \(Creation date: [0-9]{4}-[0-9]{2}-[0-9]{2}, number of genomes: 90, number of BUSCOs: 1013\)
-# Summarized benchmarking in BUSCO notation for file [a-z0-9_\-/\.]+
-# BUSCO was run in mode: euk_genome_met
-# Gene predictor used: metaeuk
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
+# Summarized benchmarking in BUSCO notation for file /tmp/tmpl5l1blpe/files/f/3/1/dataset_f31d44e3-c824-4cdf-92ba-99a2c26071d2.dat
+# BUSCO was run in mode: euk_genome_min
+# Gene predictor used: miniprot
 
-	\*\*\*\*\* Results: \*\*\*\*\*
+	***** Results: *****
 
-	C:0\.2%\[S:0\.2%,D:0\.0%\],F:0\.0%,M:99\.8%,n:1013	   
-	2	Complete BUSCOs \(C\)			   
-	2	Complete and single-copy BUSCOs \(S\)	   
-	0	Complete and duplicated BUSCOs \(D\)	   
-	0	Fragmented BUSCOs \(F\)			   
-	1011	Missing BUSCOs \(M\)			   
+	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013	   
+	1	Complete BUSCOs (C)			   
+	1	Complete and single-copy BUSCOs (S)	   
+	0	Complete and duplicated BUSCOs (D)	   
+	0	Fragmented BUSCOs (F)			   
+	1012	Missing BUSCOs (M)			   
 	1013	Total BUSCO groups searched		   
 
 Assembly Statistics:
 	1	Number of scaffolds
 	1	Number of contigs
 	62370	Total length
-	0\.000%	Percent gaps
+	0.000%	Percent gaps
 	62 KB	Scaffold N50
 	62 KB	Contigs N50
 
 
 Dependencies and versions:
-	hmmsearch: [0-9\.\+]+
-	bbtools: [0-9\.\+]+
-	metaeuk: [0-9a-z\.\+]+
-	busco: [0-9\.\+]+
+	hmmsearch: 3.1
+	bbtools: 39.06
+	miniprot_index: 0.13-r248
+	miniprot_align: 0.13-r248
+	python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0)
+	busco: 5.7.1
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk/summary.png
Binary file test-data/genome_results_metaeuk/summary.png has changed
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk_auto/full_table
--- a/test-data/genome_results_metaeuk_auto/full_table	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/genome_results_metaeuk_auto/full_table	Fri Aug 30 15:19:56 2024 +0000
@@ -1,6 +1,6 @@
-# BUSCO version is: 5.5.0 
-# The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255)
-# Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: eukaryota_odb10 (Creation date: 2024-01-08, number of genomes: 70, number of BUSCOs: 255)
+# Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
 39650at2759	Missing
 83779at2759	Missing
 87842at2759	Missing
@@ -131,7 +131,7 @@
 1041560at2759	Missing
 1049599at2759	Missing
 1051021at2759	Missing
-1053181at2759	Complete	sample:35678-34845	34845	35678	-	45.0	149
+1053181at2759	Complete	sample	35693	34845	-	44.7	149	https://v10-1.orthodb.org/?query=1053181at2759	Checkpoint protein Hus1/Mec3
 1057950at2759	Missing
 1065019at2759	Missing
 1076134at2759	Missing
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk_auto/missing_buscos_list
--- a/test-data/genome_results_metaeuk_auto/missing_buscos_list	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/genome_results_metaeuk_auto/missing_buscos_list	Fri Aug 30 15:19:56 2024 +0000
@@ -1,5 +1,5 @@
-# BUSCO version is: 5.5.0 
-# The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255)
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: eukaryota_odb10 (Creation date: 2024-01-08, number of genomes: 70, number of BUSCOs: 255)
 # Busco id
 1001705at2759
 1003258at2759
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk_auto/out.gff
--- a/test-data/genome_results_metaeuk_auto/out.gff	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/genome_results_metaeuk_auto/out.gff	Fri Aug 30 15:19:56 2024 +0000
@@ -1,5 +1,2 @@
 ##gff-version 3
 sample	MetaEuk	gene	34846	35694	527	-	.	Target_ID=1053181at2759_7245_0:00200b;TCS_ID=1053181at2759_7245_0:00200b|sample|-|34845
-sample	MetaEuk	mRNA	34846	35694	527	-	.	Target_ID=1053181at2759_7245_0:00200b;TCS_ID=1053181at2759_7245_0:00200b|sample|-|34845_mRNA;Parent=1053181at2759_7245_0:00200b|sample|-|34845
-sample	MetaEuk	exon	34846	35694	527	-	.	Target_ID=1053181at2759_7245_0:00200b;TCS_ID=1053181at2759_7245_0:00200b|sample|-|34845_exon_0;Parent=1053181at2759_7245_0:00200b|sample|-|34845_mRNA
-sample	MetaEuk	CDS	34846	35694	527	-	.	Target_ID=1053181at2759_7245_0:00200b;TCS_ID=1053181at2759_7245_0:00200b|sample|-|34845_CDS_0;Parent=1053181at2759_7245_0:00200b|sample|-|34845_exon_0
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk_auto/short_summary
--- a/test-data/genome_results_metaeuk_auto/short_summary	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/genome_results_metaeuk_auto/short_summary	Fri Aug 30 15:19:56 2024 +0000
@@ -1,6 +1,6 @@
-# BUSCO version is: 5.5.0 
-# The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmp5_syjrgy/files/a/5/a/dataset_a5adf25d-f667-41d6-9472-f8661403e128.dat
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: eukaryota_odb10 (Creation date: 2024-01-08, number of genomes: 70, number of BUSCOs: 255)
+# Summarized benchmarking in BUSCO notation for file /tmp/tmpg41og118/files/f/5/e/dataset_f5e13834-6f57-4cb4-af82-b730a3e03fdb.dat
 # BUSCO was run in mode: euk_genome_met
 # Gene predictor used: metaeuk
 
@@ -25,7 +25,8 @@
 
 Dependencies and versions:
 	hmmsearch: 3.1
-	bbtools: 39.01
+	bbtools: 39.06
 	prodigal: 2.6.3
-	busco: 5.5.0
-	metaeuk: 6.a5d39d9
+	python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0)
+	busco: 5.7.1
+	metaeuk: 7.bba0d80
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk_auto/summary.png
Binary file test-data/genome_results_metaeuk_auto/summary.png has changed
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_miniprot/full_table
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results_miniprot/full_table	Fri Aug 30 15:19:56 2024 +0000
@@ -0,0 +1,1016 @@
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
+# Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
+774at6656	Missing
+980at6656	Missing
+997at6656	Missing
+1166at6656	Missing
+1885at6656	Missing
+1990at6656	Missing
+2148at6656	Missing
+2456at6656	Missing
+2473at6656	Missing
+3310at6656	Missing
+3585at6656	Missing
+3644at6656	Missing
+4136at6656	Missing
+4227at6656	Missing
+4864at6656	Missing
+5277at6656	Missing
+5616at6656	Missing
+6453at6656	Missing
+6563at6656	Missing
+6715at6656	Missing
+6820at6656	Missing
+7210at6656	Missing
+8145at6656	Missing
+8495at6656	Missing
+8847at6656	Missing
+8913at6656	Missing
+9647at6656	Missing
+9648at6656	Missing
+10240at6656	Missing
+10573at6656	Missing
+11384at6656	Missing
+12029at6656	Missing
+12174at6656	Missing
+12383at6656	Missing
+12771at6656	Missing
+12846at6656	Missing
+13019at6656	Missing
+13051at6656	Missing
+13736at6656	Missing
+13833at6656	Missing
+13858at6656	Missing
+13890at6656	Missing
+13934at6656	Missing
+14090at6656	Missing
+14257at6656	Missing
+14447at6656	Missing
+14995at6656	Missing
+15200at6656	Missing
+15697at6656	Missing
+15905at6656	Missing
+16061at6656	Missing
+16084at6656	Missing
+16220at6656	Missing
+16630at6656	Missing
+16648at6656	Missing
+17096at6656	Missing
+17122at6656	Missing
+17128at6656	Missing
+17748at6656	Missing
+18036at6656	Missing
+18055at6656	Missing
+18073at6656	Missing
+18630at6656	Missing
+18929at6656	Missing
+19044at6656	Missing
+19058at6656	Missing
+19104at6656	Missing
+19129at6656	Missing
+19208at6656	Missing
+19289at6656	Missing
+19590at6656	Missing
+19760at6656	Missing
+20093at6656	Missing
+20162at6656	Missing
+20267at6656	Missing
+20935at6656	Missing
+20936at6656	Missing
+21019at6656	Missing
+21191at6656	Missing
+21361at6656	Missing
+21367at6656	Missing
+21385at6656	Missing
+22098at6656	Missing
+22148at6656	Missing
+22358at6656	Missing
+22364at6656	Missing
+22468at6656	Missing
+22611at6656	Missing
+22887at6656	Missing
+23309at6656	Missing
+23388at6656	Missing
+23429at6656	Missing
+23917at6656	Missing
+24255at6656	Missing
+24427at6656	Missing
+24459at6656	Missing
+24556at6656	Missing
+24573at6656	Missing
+25554at6656	Missing
+25680at6656	Missing
+26078at6656	Missing
+26653at6656	Missing
+26734at6656	Missing
+27198at6656	Missing
+27515at6656	Missing
+27617at6656	Missing
+27655at6656	Missing
+28325at6656	Missing
+28380at6656	Missing
+28519at6656	Missing
+28685at6656	Missing
+28872at6656	Missing
+29213at6656	Missing
+29237at6656	Missing
+29365at6656	Missing
+29730at6656	Missing
+29744at6656	Missing
+30156at6656	Missing
+30184at6656	Missing
+30267at6656	Missing
+30463at6656	Missing
+30512at6656	Missing
+30526at6656	Missing
+30642at6656	Missing
+30822at6656	Missing
+30918at6656	Missing
+30962at6656	Missing
+31014at6656	Missing
+31119at6656	Missing
+31196at6656	Missing
+31333at6656	Missing
+31480at6656	Missing
+31615at6656	Missing
+31634at6656	Missing
+31820at6656	Missing
+31886at6656	Missing
+31919at6656	Missing
+32694at6656	Missing
+32733at6656	Missing
+32851at6656	Missing
+33187at6656	Missing
+33566at6656	Missing
+33794at6656	Missing
+34586at6656	Missing
+34917at6656	Missing
+35035at6656	Missing
+35548at6656	Missing
+35680at6656	Missing
+35708at6656	Missing
+35995at6656	Missing
+36374at6656	Missing
+36387at6656	Missing
+36403at6656	Missing
+36463at6656	Missing
+37030at6656	Missing
+37297at6656	Missing
+37387at6656	Missing
+37678at6656	Missing
+38140at6656	Missing
+38186at6656	Missing
+38303at6656	Missing
+38391at6656	Missing
+38567at6656	Missing
+38819at6656	Missing
+38928at6656	Missing
+39506at6656	Missing
+39548at6656	Missing
+39783at6656	Missing
+39809at6656	Missing
+39821at6656	Missing
+40065at6656	Missing
+40092at6656	Missing
+40213at6656	Missing
+40240at6656	Missing
+40319at6656	Missing
+40323at6656	Missing
+40399at6656	Missing
+40691at6656	Missing
+40929at6656	Missing
+41522at6656	Missing
+41990at6656	Missing
+42577at6656	Missing
+42622at6656	Missing
+42819at6656	Missing
+42842at6656	Missing
+42929at6656	Missing
+42943at6656	Missing
+42992at6656	Missing
+43045at6656	Missing
+43236at6656	Missing
+43245at6656	Missing
+43540at6656	Missing
+43728at6656	Missing
+43774at6656	Missing
+44001at6656	Missing
+44123at6656	Missing
+44359at6656	Missing
+44389at6656	Missing
+44504at6656	Missing
+44630at6656	Missing
+44694at6656	Missing
+44953at6656	Missing
+45131at6656	Missing
+45367at6656	Missing
+45528at6656	Missing
+45556at6656	Missing
+45732at6656	Missing
+45915at6656	Missing
+46430at6656	Missing
+46437at6656	Missing
+46671at6656	Missing
+46679at6656	Missing
+46692at6656	Missing
+46750at6656	Missing
+46960at6656	Missing
+47270at6656	Missing
+47443at6656	Missing
+47495at6656	Missing
+47500at6656	Missing
+47967at6656	Missing
+48195at6656	Missing
+48466at6656	Missing
+48519at6656	Missing
+48657at6656	Missing
+48836at6656	Missing
+49070at6656	Missing
+49526at6656	Missing
+49936at6656	Missing
+50191at6656	Missing
+50493at6656	Missing
+50740at6656	Missing
+50792at6656	Missing
+50947at6656	Missing
+51037at6656	Missing
+51280at6656	Missing
+51364at6656	Missing
+51757at6656	Missing
+52210at6656	Missing
+52224at6656	Missing
+52320at6656	Missing
+52422at6656	Missing
+52643at6656	Missing
+52828at6656	Missing
+53201at6656	Missing
+53243at6656	Missing
+53298at6656	Missing
+53318at6656	Missing
+53993at6656	Missing
+54236at6656	Missing
+54527at6656	Missing
+54679at6656	Missing
+55036at6656	Missing
+55094at6656	Missing
+55108at6656	Missing
+55260at6656	Missing
+55417at6656	Missing
+55450at6656	Missing
+55599at6656	Missing
+55847at6656	Missing
+55932at6656	Missing
+55953at6656	Missing
+56010at6656	Missing
+56322at6656	Missing
+56449at6656	Missing
+56523at6656	Missing
+56687at6656	Missing
+56836at6656	Missing
+57262at6656	Missing
+57597at6656	Missing
+57605at6656	Missing
+57624at6656	Missing
+57932at6656	Missing
+58012at6656	Missing
+58027at6656	Missing
+58110at6656	Missing
+58119at6656	Missing
+58276at6656	Missing
+59084at6656	Missing
+59193at6656	Missing
+59197at6656	Missing
+59200at6656	Missing
+59226at6656	Missing
+59393at6656	Missing
+59430at6656	Missing
+59681at6656	Missing
+59824at6656	Missing
+59833at6656	Missing
+60067at6656	Missing
+60299at6656	Missing
+60333at6656	Missing
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+60682at6656	Missing
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+60750at6656	Missing
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+61081at6656	Missing
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+61153at6656	Missing
+61180at6656	Missing
+61261at6656	Missing
+61577at6656	Missing
+61612at6656	Missing
+62010at6656	Missing
+62275at6656	Missing
+62580at6656	Missing
+62678at6656	Missing
+62914at6656	Missing
+62979at6656	Missing
+63193at6656	Missing
+63228at6656	Missing
+63461at6656	Missing
+63923at6656	Missing
+63924at6656	Missing
+64046at6656	Missing
+64896at6656	Missing
+65490at6656	Missing
+65508at6656	Missing
+65532at6656	Missing
+65949at6656	Missing
+66028at6656	Missing
+66229at6656	Missing
+66299at6656	Missing
+66366at6656	Missing
+66597at6656	Missing
+66770at6656	Missing
+67113at6656	Missing
+67166at6656	Missing
+67191at6656	Missing
+67491at6656	Missing
+67583at6656	Missing
+67710at6656	Missing
+68468at6656	Missing
+68491at6656	Missing
+68731at6656	Missing
+68876at6656	Missing
+68939at6656	Missing
+68961at6656	Missing
+68981at6656	Missing
+68987at6656	Missing
+69201at6656	Missing
+69238at6656	Missing
+69284at6656	Missing
+69394at6656	Missing
+69403at6656	Missing
+69742at6656	Missing
+69897at6656	Missing
+70078at6656	Missing
+70201at6656	Missing
+70300at6656	Missing
+70550at6656	Missing
+70663at6656	Missing
+71018at6656	Missing
+71110at6656	Missing
+71129at6656	Missing
+71199at6656	Missing
+71230at6656	Missing
+71251at6656	Missing
+71483at6656	Missing
+71937at6656	Missing
+72450at6656	Missing
+72578at6656	Missing
+72583at6656	Missing
+72586at6656	Missing
+72782at6656	Missing
+72857at6656	Missing
+73084at6656	Missing
+73301at6656	Missing
+73455at6656	Missing
+73456at6656	Missing
+73547at6656	Missing
+74030at6656	Missing
+74384at6656	Missing
+74655at6656	Missing
+74692at6656	Missing
+74836at6656	Missing
+75692at6656	Missing
+75704at6656	Missing
+75764at6656	Missing
+75982at6656	Missing
+76308at6656	Missing
+76342at6656	Missing
+76573at6656	Missing
+76745at6656	Missing
+76812at6656	Missing
+77197at6656	Missing
+77688at6656	Missing
+77770at6656	Missing
+77883at6656	Missing
+77976at6656	Missing
+77987at6656	Missing
+78110at6656	Missing
+78202at6656	Missing
+78254at6656	Missing
+78695at6656	Missing
+78758at6656	Missing
+78777at6656	Missing
+78844at6656	Missing
+78854at6656	Missing
+78919at6656	Missing
+78921at6656	Missing
+78947at6656	Missing
+78968at6656	Missing
+79241at6656	Missing
+79377at6656	Missing
+79915at6656	Missing
+79993at6656	Missing
+80067at6656	Missing
+80294at6656	Missing
+80317at6656	Missing
+80348at6656	Missing
+80689at6656	Missing
+80693at6656	Missing
+80948at6656	Missing
+81292at6656	Missing
+81307at6656	Missing
+81406at6656	Missing
+81413at6656	Missing
+81423at6656	Missing
+81650at6656	Missing
+81703at6656	Missing
+81708at6656	Missing
+81919at6656	Missing
+81950at6656	Missing
+83102at6656	Missing
+83164at6656	Missing
+83303at6656	Missing
+83350at6656	Missing
+83372at6656	Missing
+83376at6656	Missing
+83613at6656	Missing
+83673at6656	Missing
+83755at6656	Missing
+83765at6656	Missing
+84028at6656	Missing
+84097at6656	Missing
+84149at6656	Missing
+84169at6656	Missing
+84422at6656	Missing
+84576at6656	Missing
+84819at6656	Missing
+84925at6656	Missing
+85103at6656	Missing
+85509at6656	Missing
+85574at6656	Missing
+85680at6656	Missing
+85810at6656	Missing
+86262at6656	Missing
+86318at6656	Missing
+86488at6656	Missing
+86654at6656	Missing
+86715at6656	Missing
+86889at6656	Missing
+86930at6656	Missing
+87014at6656	Missing
+87089at6656	Missing
+87103at6656	Missing
+87114at6656	Missing
+87139at6656	Missing
+87142at6656	Missing
+87527at6656	Missing
+87575at6656	Missing
+87695at6656	Missing
+87728at6656	Missing
+87910at6656	Missing
+87928at6656	Missing
+87933at6656	Missing
+88051at6656	Missing
+88711at6656	Missing
+89064at6656	Missing
+89153at6656	Missing
+89677at6656	Missing
+89713at6656	Missing
+89810at6656	Missing
+89840at6656	Missing
+89864at6656	Missing
+90126at6656	Missing
+90322at6656	Missing
+90580at6656	Missing
+90600at6656	Missing
+90822at6656	Missing
+90928at6656	Missing
+90931at6656	Missing
+91002at6656	Missing
+91005at6656	Missing
+91022at6656	Missing
+91313at6656	Missing
+91418at6656	Missing
+91468at6656	Missing
+91933at6656	Missing
+91946at6656	Missing
+92167at6656	Missing
+92184at6656	Missing
+92420at6656	Missing
+92576at6656	Missing
+92777at6656	Missing
+92854at6656	Missing
+93061at6656	Missing
+93085at6656	Missing
+93152at6656	Missing
+93168at6656	Missing
+93408at6656	Missing
+93432at6656	Missing
+93483at6656	Missing
+93507at6656	Missing
+93535at6656	Missing
+93797at6656	Missing
+94054at6656	Missing
+94238at6656	Complete	sample	35679	34845	-	60.7	116	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
+94263at6656	Missing
+94304at6656	Missing
+94473at6656	Missing
+94476at6656	Missing
+94842at6656	Missing
+94878at6656	Missing
+95028at6656	Missing
+95089at6656	Missing
+95294at6656	Missing
+95524at6656	Missing
+96251at6656	Missing
+96444at6656	Missing
+96569at6656	Missing
+96592at6656	Missing
+96601at6656	Missing
+96956at6656	Missing
+96971at6656	Missing
+97225at6656	Missing
+97492at6656	Missing
+97749at6656	Missing
+97763at6656	Missing
+97865at6656	Missing
+98066at6656	Missing
+98251at6656	Missing
+98544at6656	Missing
+98620at6656	Missing
+98725at6656	Missing
+98755at6656	Missing
+98821at6656	Missing
+98845at6656	Missing
+98927at6656	Missing
+98948at6656	Missing
+99204at6656	Missing
+99270at6656	Missing
+99307at6656	Missing
+99377at6656	Missing
+99519at6656	Missing
+99625at6656	Missing
+99998at6656	Missing
+100070at6656	Missing
+100136at6656	Missing
+100216at6656	Missing
+100227at6656	Missing
+100296at6656	Missing
+100612at6656	Missing
+100664at6656	Missing
+100673at6656	Missing
+100760at6656	Missing
+101349at6656	Missing
+101359at6656	Missing
+101491at6656	Missing
+101531at6656	Missing
+101621at6656	Missing
+101727at6656	Missing
+101761at6656	Missing
+101767at6656	Missing
+101829at6656	Missing
+101886at6656	Missing
+102321at6656	Missing
+102714at6656	Missing
+102770at6656	Missing
+103125at6656	Missing
+103207at6656	Missing
+103479at6656	Missing
+103590at6656	Missing
+103747at6656	Missing
+103749at6656	Missing
+103752at6656	Missing
+103908at6656	Missing
+103914at6656	Missing
+104063at6656	Missing
+104122at6656	Missing
+104198at6656	Missing
+104410at6656	Missing
+104588at6656	Missing
+104595at6656	Missing
+104604at6656	Missing
+104769at6656	Missing
+104898at6656	Missing
+105000at6656	Missing
+105099at6656	Missing
+105170at6656	Missing
+105364at6656	Missing
+105457at6656	Missing
+105771at6656	Missing
+105887at6656	Missing
+106116at6656	Missing
+106126at6656	Missing
+106466at6656	Missing
+106470at6656	Missing
+106634at6656	Missing
+106639at6656	Missing
+106788at6656	Missing
+106988at6656	Missing
+107030at6656	Missing
+107139at6656	Missing
+107226at6656	Missing
+107353at6656	Missing
+107427at6656	Missing
+107453at6656	Missing
+107615at6656	Missing
+107802at6656	Missing
+107806at6656	Missing
+107844at6656	Missing
+108162at6656	Missing
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+108240at6656	Missing
+108693at6656	Missing
+108702at6656	Missing
+108705at6656	Missing
+108808at6656	Missing
+109131at6656	Missing
+109174at6656	Missing
+109325at6656	Missing
+109444at6656	Missing
+109484at6656	Missing
+109562at6656	Missing
+109664at6656	Missing
+109724at6656	Missing
+109793at6656	Missing
+109919at6656	Missing
+109923at6656	Missing
+110129at6656	Missing
+110504at6656	Missing
+110787at6656	Missing
+110982at6656	Missing
+111082at6656	Missing
+111153at6656	Missing
+111236at6656	Missing
+111239at6656	Missing
+111545at6656	Missing
+111851at6656	Missing
+112281at6656	Missing
+112328at6656	Missing
+112360at6656	Missing
+112556at6656	Missing
+112634at6656	Missing
+112645at6656	Missing
+112759at6656	Missing
+113015at6656	Missing
+113300at6656	Missing
+113432at6656	Missing
+113604at6656	Missing
+113622at6656	Missing
+113641at6656	Missing
+113668at6656	Missing
+113713at6656	Missing
+113817at6656	Missing
+113818at6656	Missing
+113865at6656	Missing
+113960at6656	Missing
+114019at6656	Missing
+114360at6656	Missing
+114463at6656	Missing
+114609at6656	Missing
+114738at6656	Missing
+114765at6656	Missing
+115001at6656	Missing
+115208at6656	Missing
+115229at6656	Missing
+115252at6656	Missing
+115256at6656	Missing
+115462at6656	Missing
+115537at6656	Missing
+115841at6656	Missing
+115917at6656	Missing
+115959at6656	Missing
+115986at6656	Missing
+116117at6656	Missing
+116401at6656	Missing
+116608at6656	Missing
+116688at6656	Missing
+116804at6656	Missing
+116982at6656	Missing
+117173at6656	Missing
+117335at6656	Missing
+117399at6656	Missing
+117413at6656	Missing
+117586at6656	Missing
+117742at6656	Missing
+117811at6656	Missing
+117843at6656	Missing
+117947at6656	Missing
+118014at6656	Missing
+118037at6656	Missing
+118496at6656	Missing
+118527at6656	Missing
+118761at6656	Missing
+118780at6656	Missing
+118807at6656	Missing
+118831at6656	Missing
+118904at6656	Missing
+119012at6656	Missing
+119144at6656	Missing
+119188at6656	Missing
+119194at6656	Missing
+119438at6656	Missing
+119541at6656	Missing
+119951at6656	Missing
+120047at6656	Missing
+120383at6656	Missing
+120445at6656	Missing
+120875at6656	Missing
+120907at6656	Missing
+120958at6656	Missing
+121002at6656	Missing
+121220at6656	Missing
+121530at6656	Missing
+121558at6656	Missing
+121847at6656	Missing
+121894at6656	Missing
+122526at6656	Missing
+122665at6656	Missing
+122816at6656	Missing
+123035at6656	Missing
+123320at6656	Missing
+123409at6656	Missing
+123631at6656	Missing
+123672at6656	Missing
+123790at6656	Missing
+123793at6656	Missing
+123853at6656	Missing
+124174at6656	Missing
+124282at6656	Missing
+124400at6656	Missing
+124452at6656	Missing
+124628at6656	Missing
+124707at6656	Missing
+124720at6656	Missing
+124730at6656	Missing
+124981at6656	Missing
+125100at6656	Missing
+125127at6656	Missing
+125210at6656	Missing
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+125238at6656	Missing
+125414at6656	Missing
+125446at6656	Missing
+125452at6656	Missing
+125716at6656	Missing
+126074at6656	Missing
+126225at6656	Missing
+126442at6656	Missing
+126483at6656	Missing
+126733at6656	Missing
+127349at6656	Missing
+127511at6656	Missing
+127602at6656	Missing
+127649at6656	Missing
+127661at6656	Missing
+127775at6656	Missing
+127998at6656	Missing
+128030at6656	Missing
+128188at6656	Missing
+128216at6656	Missing
+128331at6656	Missing
+128464at6656	Missing
+128916at6656	Missing
+129077at6656	Missing
+129131at6656	Missing
+129200at6656	Missing
+129593at6656	Missing
+129618at6656	Missing
+129675at6656	Missing
+129886at6656	Missing
+129902at6656	Missing
+129989at6656	Missing
+130105at6656	Missing
+130126at6656	Missing
+130176at6656	Missing
+130363at6656	Missing
+130514at6656	Missing
+130563at6656	Missing
+130663at6656	Missing
+130825at6656	Missing
+130923at6656	Missing
+131276at6656	Missing
+131307at6656	Missing
+131495at6656	Missing
+131516at6656	Missing
+131588at6656	Missing
+131642at6656	Missing
+131668at6656	Missing
+131720at6656	Missing
+131751at6656	Missing
+131921at6656	Missing
+132329at6656	Missing
+132340at6656	Missing
+132441at6656	Missing
+132495at6656	Missing
+132760at6656	Missing
+132854at6656	Missing
+132857at6656	Missing
+133015at6656	Missing
+133329at6656	Missing
+133362at6656	Missing
+133422at6656	Missing
+133603at6656	Missing
+133735at6656	Missing
+133949at6656	Missing
+134073at6656	Missing
+134209at6656	Missing
+134216at6656	Missing
+134673at6656	Missing
+134708at6656	Missing
+134776at6656	Missing
+134835at6656	Missing
+134853at6656	Missing
+134865at6656	Missing
+134885at6656	Missing
+135065at6656	Missing
+135075at6656	Missing
+135107at6656	Missing
+135123at6656	Missing
+135203at6656	Missing
+135204at6656	Missing
+135215at6656	Missing
+135357at6656	Missing
+135373at6656	Missing
+135391at6656	Missing
+135526at6656	Missing
+135676at6656	Missing
+135690at6656	Missing
+135702at6656	Missing
+135764at6656	Missing
+135828at6656	Missing
+135834at6656	Missing
+135859at6656	Missing
+135975at6656	Missing
+135994at6656	Missing
+136055at6656	Missing
+136095at6656	Missing
+136119at6656	Missing
+136224at6656	Missing
+136365at6656	Missing
+136559at6656	Missing
+136888at6656	Missing
+137050at6656	Missing
+137197at6656	Missing
+137202at6656	Missing
+137334at6656	Missing
+137338at6656	Missing
+137422at6656	Missing
+137609at6656	Missing
+137688at6656	Missing
+137709at6656	Missing
+137711at6656	Missing
+138243at6656	Missing
+138271at6656	Missing
+138379at6656	Missing
+138401at6656	Missing
+138502at6656	Missing
+138553at6656	Missing
+138659at6656	Missing
+138684at6656	Missing
+138937at6656	Missing
+139217at6656	Missing
+139553at6656	Missing
+139638at6656	Missing
+139744at6656	Missing
+139834at6656	Missing
+140076at6656	Missing
+140197at6656	Missing
+140198at6656	Missing
+140403at6656	Missing
+140461at6656	Missing
+140693at6656	Missing
+140874at6656	Missing
+140903at6656	Missing
+141031at6656	Missing
+141163at6656	Missing
+141166at6656	Missing
+141175at6656	Missing
+141298at6656	Missing
+141804at6656	Missing
+141859at6656	Missing
+141916at6656	Missing
+142388at6656	Missing
+142415at6656	Missing
+142522at6656	Missing
+142613at6656	Missing
+142661at6656	Missing
+142833at6656	Missing
+143154at6656	Missing
+143279at6656	Missing
+143459at6656	Missing
+143489at6656	Missing
+143562at6656	Missing
+143626at6656	Missing
+143709at6656	Missing
+143812at6656	Missing
+143930at6656	Missing
+144337at6656	Missing
+144652at6656	Missing
+144836at6656	Missing
+144851at6656	Missing
+144853at6656	Missing
+145033at6656	Missing
+145102at6656	Missing
+145443at6656	Missing
+145610at6656	Missing
+145811at6656	Missing
+145996at6656	Missing
+146007at6656	Missing
+146036at6656	Missing
+146087at6656	Missing
+146102at6656	Missing
+146103at6656	Missing
+146383at6656	Missing
+146600at6656	Missing
+146920at6656	Missing
+147002at6656	Missing
+147025at6656	Missing
+147322at6656	Missing
+147657at6656	Missing
+147723at6656	Missing
+147852at6656	Missing
+147891at6656	Missing
+147980at6656	Missing
+148134at6656	Missing
+148619at6656	Missing
+148713at6656	Missing
+148851at6656	Missing
+148890at6656	Missing
+149101at6656	Missing
+149126at6656	Missing
+149251at6656	Missing
+149405at6656	Missing
+149680at6656	Missing
+149753at6656	Missing
+149796at6656	Missing
+149819at6656	Missing
+149973at6656	Missing
+149977at6656	Missing
+150005at6656	Missing
+150049at6656	Missing
+150137at6656	Missing
+150182at6656	Missing
+150251at6656	Missing
+150327at6656	Missing
+150479at6656	Missing
+150583at6656	Missing
+150585at6656	Missing
+150667at6656	Missing
+150765at6656	Missing
+151102at6656	Missing
+151111at6656	Missing
+151114at6656	Missing
+151393at6656	Missing
+151436at6656	Missing
+151642at6656	Missing
+151658at6656	Missing
+152032at6656	Missing
+152109at6656	Missing
+152402at6656	Missing
+152534at6656	Missing
+152871at6656	Missing
+153155at6656	Missing
+153232at6656	Missing
+153312at6656	Missing
+153534at6656	Missing
+153693at6656	Missing
+153873at6656	Missing
+154133at6656	Missing
+154415at6656	Missing
+154507at6656	Missing
+155285at6656	Missing
+156057at6656	Missing
+156081at6656	Missing
+156111at6656	Missing
+156305at6656	Missing
+156395at6656	Missing
+156728at6656	Missing
+156824at6656	Missing
+156882at6656	Missing
+156975at6656	Missing
+157486at6656	Missing
+157579at6656	Missing
+157851at6656	Missing
+157879at6656	Missing
+158194at6656	Missing
+158760at6656	Missing
+159231at6656	Missing
+159420at6656	Missing
+159542at6656	Missing
+160675at6656	Missing
+160705at6656	Missing
+161435at6656	Missing
+162059at6656	Missing
+162147at6656	Missing
+162594at6656	Missing
+162628at6656	Missing
+162841at6656	Missing
+163670at6656	Missing
+163896at6656	Missing
+164354at6656	Missing
+164512at6656	Missing
+165142at6656	Missing
+165207at6656	Missing
+165493at6656	Missing
+166476at6656	Missing
+166479at6656	Missing
+166485at6656	Missing
+169220at6656	Missing
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_miniprot/out.gff
diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_miniprot/short_summary
diff -r ea8146ee148f -r 2babe6d5c561 test-data/proteome_results/full_table
--- a/test-data/proteome_results/full_table	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/proteome_results/full_table	Fri Aug 30 15:19:56 2024 +0000
@@ -1,5 +1,5 @@
-# BUSCO version is: 5.5.0 
-# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Score	Length	OrthoDB url	Description
 774at6656	Missing
 980at6656	Missing
@@ -86,7 +86,7 @@
 22098at6656	Missing
 22148at6656	Missing
 22358at6656	Missing
-22364at6656	Complete	BUSCOaEOG7B0HST	1355.6	788	https://www.orthodb.org/v10?query=22364at6656	importin-5
+22364at6656	Complete	BUSCOaEOG7B0HST	1355.6	788	https://v10-1.orthodb.org/?query=22364at6656	Importin repeat 4
 22468at6656	Missing
 22611at6656	Missing
 22887at6656	Missing
diff -r ea8146ee148f -r 2babe6d5c561 test-data/proteome_results/missing_buscos_list
--- a/test-data/proteome_results/missing_buscos_list	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/proteome_results/missing_buscos_list	Fri Aug 30 15:19:56 2024 +0000
@@ -1,5 +1,5 @@
-# BUSCO version is: 5.5.0 
-# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
 100136at6656
diff -r ea8146ee148f -r 2babe6d5c561 test-data/proteome_results/short_summary
--- a/test-data/proteome_results/short_summary	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/proteome_results/short_summary	Fri Aug 30 15:19:56 2024 +0000
@@ -1,18 +1,19 @@
-# BUSCO version is: 5\.5\.0 
-# The lineage dataset is: arthropoda_odb10 \(Creation date: [0-9]{4}-[0-9]{2}-[0-9]{2}, number of genomes: 90, number of BUSCOs: 1013\)
-# Summarized benchmarking in BUSCO notation for file [a-z0-9_\-/\.]+
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
+# Summarized benchmarking in BUSCO notation for file /tmp/tmpl5l1blpe/files/e/0/f/dataset_e0f4947a-b95c-45dc-bee8-301d13fe1fe5.dat
 # BUSCO was run in mode: proteins
 
-	\*\*\*\*\* Results: \*\*\*\*\*
+	***** Results: *****
 
-	C:0\.1%\[S:0\.1%,D:0\.0%\],F:0\.0%,M:99\.9%,n:1013	   
-	1	Complete BUSCOs \(C\)			   
-	1	Complete and single-copy BUSCOs \(S\)	   
-	0	Complete and duplicated BUSCOs \(D\)	   
-	0	Fragmented BUSCOs \(F\)			   
-	1012	Missing BUSCOs \(M\)			   
+	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013	   
+	1	Complete BUSCOs (C)			   
+	1	Complete and single-copy BUSCOs (S)	   
+	0	Complete and duplicated BUSCOs (D)	   
+	0	Fragmented BUSCOs (F)			   
+	1012	Missing BUSCOs (M)			   
 	1013	Total BUSCO groups searched		   
 
 Dependencies and versions:
-	hmmsearch: [0-9\.\+]+
-	busco: [0-9\.\+]+
+	hmmsearch: 3.1
+	python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0)
+	busco: 5.7.1
diff -r ea8146ee148f -r 2babe6d5c561 test-data/proteome_results/summary.png
Binary file test-data/proteome_results/summary.png has changed
diff -r ea8146ee148f -r 2babe6d5c561 test-data/test-db/busco_downloads/lineages/archaea_odb10/refseq_db.faa
diff -r ea8146ee148f -r 2babe6d5c561 test-data/transcriptome_results/full_table
--- a/test-data/transcriptome_results/full_table	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/transcriptome_results/full_table	Fri Aug 30 15:19:56 2024 +0000
@@ -1,5 +1,5 @@
-# BUSCO version is: 5.5.0 
-# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Score	Length	OrthoDB url	Description
 774at6656	Missing
 980at6656	Missing
@@ -86,7 +86,7 @@
 22098at6656	Missing
 22148at6656	Missing
 22358at6656	Missing
-22364at6656	Complete	BUSCOaEOG7B0HST:0-2699	1355.6	788	https://www.orthodb.org/v10?query=22364at6656	importin-5
+22364at6656	Complete	BUSCOaEOG7B0HST:0-2699	1355.6	788	https://v10-1.orthodb.org/?query=22364at6656	Importin repeat 4
 22468at6656	Missing
 22611at6656	Missing
 22887at6656	Missing
diff -r ea8146ee148f -r 2babe6d5c561 test-data/transcriptome_results/missing_buscos_list
--- a/test-data/transcriptome_results/missing_buscos_list	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/transcriptome_results/missing_buscos_list	Fri Aug 30 15:19:56 2024 +0000
@@ -1,5 +1,5 @@
-# BUSCO version is: 5.5.0 
-# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
 100136at6656
diff -r ea8146ee148f -r 2babe6d5c561 test-data/transcriptome_results/out.gff
--- a/test-data/transcriptome_results/out.gff	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/transcriptome_results/out.gff	Fri Aug 30 15:19:56 2024 +0000
@@ -1,5 +1,2 @@
 ##gff-version 3
 BUSCOaEOG7B0HST	MetaEuk	gene	1	2700	1493	+	.	Target_ID=22364at6656_211228_0:002349;TCS_ID=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0
-BUSCOaEOG7B0HST	MetaEuk	mRNA	1	2700	1493	+	.	Target_ID=22364at6656_211228_0:002349;TCS_ID=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_mRNA;Parent=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0
-BUSCOaEOG7B0HST	MetaEuk	exon	1	2700	1493	+	.	Target_ID=22364at6656_211228_0:002349;TCS_ID=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_exon_0;Parent=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_mRNA
-BUSCOaEOG7B0HST	MetaEuk	CDS	1	2700	1493	+	.	Target_ID=22364at6656_211228_0:002349;TCS_ID=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_CDS_0;Parent=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_exon_0
diff -r ea8146ee148f -r 2babe6d5c561 test-data/transcriptome_results/short_summary
--- a/test-data/transcriptome_results/short_summary	Mon Mar 18 16:01:49 2024 +0000
+++ b/test-data/transcriptome_results/short_summary	Fri Aug 30 15:19:56 2024 +0000
@@ -1,19 +1,20 @@
-# BUSCO version is: 5\.5\.0 
-# The lineage dataset is: arthropoda_odb10 \(Creation date: [0-9]{4}-[0-9]{2}-[0-9]{2}, number of genomes: 90, number of BUSCOs: 1013\)
-# Summarized benchmarking in BUSCO notation for file [a-z0-9_\-/\.]+
+# BUSCO version is: 5.7.1 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
+# Summarized benchmarking in BUSCO notation for file /tmp/tmpl5l1blpe/files/8/1/5/dataset_8150f803-80e8-4d16-9c33-eec04107fced.dat
 # BUSCO was run in mode: euk_tran
 
-	\*\*\*\*\* Results: \*\*\*\*\*
+	***** Results: *****
 
-	C:0\.1%\[S:0\.1%,D:0\.0%\],F:0\.0%,M:99\.9%,n:1013	   
-	1	Complete BUSCOs \(C\)			   
-	1	Complete and single-copy BUSCOs \(S\)	   
-	0	Complete and duplicated BUSCOs \(D\)	   
-	0	Fragmented BUSCOs \(F\)			   
-	1012	Missing BUSCOs \(M\)			   
+	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013	   
+	1	Complete BUSCOs (C)			   
+	1	Complete and single-copy BUSCOs (S)	   
+	0	Complete and duplicated BUSCOs (D)	   
+	0	Fragmented BUSCOs (F)			   
+	1012	Missing BUSCOs (M)			   
 	1013	Total BUSCO groups searched		   
 
 Dependencies and versions:
-	hmmsearch: [0-9\.\+]+
-	metaeuk: [0-9a-z\.\+]+
-	busco: [0-9\.\+]+
+	hmmsearch: 3.1
+	metaeuk: 7.bba0d80
+	python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0)
+	busco: 5.7.1
diff -r ea8146ee148f -r 2babe6d5c561 test-data/transcriptome_results/summary.png
Binary file test-data/transcriptome_results/summary.png has changed