deploy: 91a3708

galaxyproject · Dec 17, 2023 · 058aa70 · 058aa70
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diff --git a/404.html b/404.html
@@ -57,8 +57,8 @@
         <link rel="preload" href="/training-material/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Italic-102a.woff2" as="font" type="font/woff2" crossorigin>
 
         <link rel="preload" href="/training-material/assets/css/main.css?v=3" as="style">
-        <link rel='preload' href='/training-material/assets/js/bundle.f1f2de89.js?v=1702685401' as='script'>
-<link rel='preload' href='/training-material/assets/js/bundle.03aefefa.js?v=1702685401' as='script'>
+        <link rel='preload' href='/training-material/assets/js/bundle.f1f2de89.js?v=1702771843' as='script'>
+<link rel='preload' href='/training-material/assets/js/bundle.03aefefa.js?v=1702771843' as='script'>
         <link rel="stylesheet" href="/training-material/assets/css/main.css?v=3">
         <link rel="manifest" href="/training-material/manifest.json">
         <meta name="theme-color" content="#2c3143"/>
@@ -83,7 +83,7 @@
 
     </head>
     <body data-spy="scroll" data-target="#toc" data-brightness="auto" data-contrast="auto">
-        <script src='/training-material/assets/js/bundle.f1f2de89.js?v=1702685401'></script>
+        <script src='/training-material/assets/js/bundle.f1f2de89.js?v=1702771843'></script>
         <header>
     <nav class="navbar navbar-expand-md navbar-dark" aria-label="Site Navigation">
         <div class="container">
@@ -268,7 +268,7 @@ <h2 id="we-cant-seem-to-find-the-page-youre-looking-for">We can’t seem to find
 </footer>
 
 
-        <script src='/training-material/assets/js/bundle.03aefefa.js?v=1702685401'></script>
+        <script src='/training-material/assets/js/bundle.03aefefa.js?v=1702771843'></script>
 
     </body>
 </html>
diff --git a/accessibility.html b/accessibility.html
@@ -57,8 +57,8 @@
         <link rel="preload" href="/training-material/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Italic-102a.woff2" as="font" type="font/woff2" crossorigin>
 
         <link rel="preload" href="/training-material/assets/css/main.css?v=3" as="style">
-        <link rel='preload' href='/training-material/assets/js/bundle.f1f2de89.js?v=1702685401' as='script'>
-<link rel='preload' href='/training-material/assets/js/bundle.03aefefa.js?v=1702685401' as='script'>
+        <link rel='preload' href='/training-material/assets/js/bundle.f1f2de89.js?v=1702771843' as='script'>
+<link rel='preload' href='/training-material/assets/js/bundle.03aefefa.js?v=1702771843' as='script'>
         <link rel="stylesheet" href="/training-material/assets/css/main.css?v=3">
         <link rel="manifest" href="/training-material/manifest.json">
         <meta name="theme-color" content="#2c3143"/>
@@ -83,7 +83,7 @@
 
     </head>
     <body data-spy="scroll" data-target="#toc" data-brightness="auto" data-contrast="auto">
-        <script src='/training-material/assets/js/bundle.f1f2de89.js?v=1702685401'></script>
+        <script src='/training-material/assets/js/bundle.f1f2de89.js?v=1702771843'></script>
         <header>
     <nav class="navbar navbar-expand-md navbar-dark" aria-label="Site Navigation">
         <div class="container">
@@ -318,7 +318,7 @@ <h3 id="additional-features">Additional Features</h3>
 </footer>
 
 
-        <script src='/training-material/assets/js/bundle.03aefefa.js?v=1702685401'></script>
+        <script src='/training-material/assets/js/bundle.03aefefa.js?v=1702771843'></script>
 
     </body>
 </html>
diff --git a/all-faq.html b/all-faq.html
@@ -57,8 +57,8 @@
         <link rel="preload" href="/training-material/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Italic-102a.woff2" as="font" type="font/woff2" crossorigin>
 
         <link rel="preload" href="/training-material/assets/css/main.css?v=3" as="style">
-        <link rel='preload' href='/training-material/assets/js/bundle.f1f2de89.js?v=1702685401' as='script'>
-<link rel='preload' href='/training-material/assets/js/bundle.03aefefa.js?v=1702685401' as='script'>
+        <link rel='preload' href='/training-material/assets/js/bundle.f1f2de89.js?v=1702771843' as='script'>
+<link rel='preload' href='/training-material/assets/js/bundle.03aefefa.js?v=1702771843' as='script'>
         <link rel="stylesheet" href="/training-material/assets/css/main.css?v=3">
         <link rel="manifest" href="/training-material/manifest.json">
         <meta name="theme-color" content="#2c3143"/>
@@ -83,7 +83,7 @@
 
     </head>
     <body data-spy="scroll" data-target="#toc" data-brightness="auto" data-contrast="auto">
-        <script src='/training-material/assets/js/bundle.f1f2de89.js?v=1702685401'></script>
+        <script src='/training-material/assets/js/bundle.f1f2de89.js?v=1702771843'></script>
         <header>
     <nav class="navbar navbar-expand-md navbar-dark" aria-label="Site Navigation">
         <div class="container">
@@ -3602,7 +3602,7 @@ <h5>Still have questions?</h5>
 </footer>
 
 
-        <script src='/training-material/assets/js/bundle.03aefefa.js?v=1702685401'></script>
+        <script src='/training-material/assets/js/bundle.03aefefa.js?v=1702771843'></script>
 
     </body>
 </html>
diff --git a/api/configuration.json b/api/configuration.json
@@ -133,7 +133,7 @@
       "resources": [
         "assets/js/theme.js"
       ],
-      "timestamp": 1702685401,
+      "timestamp": 1702771843,
       "hash": "f1f2de89",
       "path": "/assets/js/bundle.f1f2de89.js"
     },
@@ -149,7 +149,7 @@
         "assets/js/[email protected]",
         "assets/js/main.js"
       ],
-      "timestamp": 1702685401,
+      "timestamp": 1702771843,
       "hash": "03aefefa",
       "path": "/assets/js/bundle.03aefefa.js"
     }
@@ -369,5 +369,5 @@
     "2023-12-01",
     "2023-11-01"
   ],
-  "age": 8.465434633812457
+  "age": 8.46817248459959
 }
diff --git a/api/psl.json b/api/psl.json
diff --git a/api/topics/assembly.json b/api/topics/assembly.json
diff --git a/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json b/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json
@@ -69,7 +69,7 @@
       "name": "Post-assembly workflow",
       "title": "Post-assembly workflow",
       "test_results": null,
-      "modified": "2023-12-16 00:10:02 +0000",
+      "modified": "2023-12-17 00:10:44 +0000",
       "mermaid": "flowchart TD\n  0[\"Input dataset\"];\n  1[\"Input parameter\"];\n  2[\"Input dataset\"];\n  3[\"Input dataset collection\"];\n  4[\"Input parameter\"];\n  5[\"Input dataset\"];\n  6[\"Input dataset\"];\n  7[\"Input dataset collection\"];\n  8[\"Input dataset collection\"];\n  9[\"Meryl\"];\n  3 -->|output| 9;\n  10[\"Collapse Collection\"];\n  3 -->|output| 10;\n  11[\"BlobToolKit\"];\n  5 -->|output| 11;\n  0 -->|output| 11;\n  2 -->|output| 11;\n  1 -->|output| 11;\n  12[\"gfastats\"];\n  5 -->|output| 12;\n  13[\"Convert compressed file to uncompressed.\"];\n  5 -->|output| 13;\n  14[\"gfastats\"];\n  5 -->|output| 14;\n  15[\"Diamond\"];\n  5 -->|output| 15;\n  6 -->|output| 15;\n  16[\"Collapse Collection\"];\n  7 -->|output| 16;\n  17[\"Collapse Collection\"];\n  8 -->|output| 17;\n  18[\"Meryl\"];\n  9 -->|read_db| 18;\n  19[\"HISAT2\"];\n  10 -->|output| 19;\n  5 -->|output| 19;\n  20[\"Smudgeplot\"];\n  10 -->|output| 20;\n  21[\"Replace\"];\n  13 -->|output1| 21;\n  22[\"Bandage Image\"];\n  14 -->|output| 22;\n  23[\"BWA-MEM2\"];\n  16 -->|output| 23;\n  5 -->|output| 23;\n  24[\"BWA-MEM2\"];\n  17 -->|output| 24;\n  5 -->|output| 24;\n  25[\"Merqury\"];\n  5 -->|output| 25;\n  18 -->|read_db| 25;\n  26[\"Meryl\"];\n  18 -->|read_db| 26;\n  27[\"Samtools stats\"];\n  19 -->|output_alignments| 27;\n  28[\"Busco\"];\n  21 -->|outfile| 28;\n  29[\"Filter and merge\"];\n  24 -->|bam_output| 29;\n  23 -->|bam_output| 29;\n  30[\"Extract dataset\"];\n  25 -->|png_files| 30;\n  31[\"Extract dataset\"];\n  25 -->|png_files| 31;\n  32[\"Extract dataset\"];\n  25 -->|png_files| 32;\n  33[\"Extract dataset\"];\n  25 -->|png_files| 33;\n  34[\"Extract dataset\"];\n  25 -->|png_files| 34;\n  35[\"GenomeScope\"];\n  26 -->|read_db_hist| 35;\n  4 -->|output| 35;\n  36[\"BlobToolKit\"];\n  15 -->|blast_tabular| 36;\n  11 -->|blobdir| 36;\n  28 -->|busco_table| 36;\n  19 -->|output_alignments| 36;\n  37[\"PretextMap\"];\n  29 -->|outfile| 37;\n  38[\"Interactive BlobToolKit\"];\n  36 -->|blobdir| 38;\n  39[\"Pretext Snapshot\"];\n  37 -->|pretext_map_out| 39;\n"
     }
   ],

diff --git a/api/topics/assembly/tutorials/assembly-quality-control/slides.json b/api/topics/assembly/tutorials/assembly-quality-control/slides.json
@@ -93,7 +93,7 @@
       "name": "Genome Assembly Quality Control",
       "title": "Genome Assembly Quality Control",
       "test_results": null,
-      "modified": "2023-12-16 00:10:02 +0000",
+      "modified": "2023-12-17 00:10:44 +0000",
       "mermaid": "flowchart TD\n  0[\"Input dataset\"];\n  1[\"Input dataset\"];\n  2[\"Input dataset\"];\n  3[\"Input dataset\"];\n  4[\"Busco\"];\n  0 -->|output| 4;\n  5[\"Busco\"];\n  1 -->|output| 5;\n  6[\"Quast\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Busco\"];\n  2 -->|output| 7;\n  8[\"Chromeister\"];\n  0 -->|output| 8;\n  2 -->|output| 8;\n  9[\"Meryl\"];\n  3 -->|output| 9;\n  10[\"Merqury\"];\n  0 -->|output| 10;\n  9 -->|read_db| 10;\n  11[\"Merqury\"];\n  1 -->|output| 11;\n  9 -->|read_db| 11;\n  12[\"Merqury\"];\n  2 -->|output| 12;\n  9 -->|read_db| 12;\n"
     }
   ],

diff --git a/api/topics/assembly/tutorials/assembly-quality-control/tutorial.json b/api/topics/assembly/tutorials/assembly-quality-control/tutorial.json
@@ -147,7 +147,7 @@
       "name": "Genome Assembly Quality Control",
       "title": "Genome Assembly Quality Control",
       "test_results": null,
-      "modified": "2023-12-16 00:10:02 +0000",
+      "modified": "2023-12-17 00:10:44 +0000",
       "mermaid": "flowchart TD\n  0[\"Input dataset\"];\n  1[\"Input dataset\"];\n  2[\"Input dataset\"];\n  3[\"Input dataset\"];\n  4[\"Busco\"];\n  0 -->|output| 4;\n  5[\"Busco\"];\n  1 -->|output| 5;\n  6[\"Quast\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Busco\"];\n  2 -->|output| 7;\n  8[\"Chromeister\"];\n  0 -->|output| 8;\n  2 -->|output| 8;\n  9[\"Meryl\"];\n  3 -->|output| 9;\n  10[\"Merqury\"];\n  0 -->|output| 10;\n  9 -->|read_db| 10;\n  11[\"Merqury\"];\n  1 -->|output| 11;\n  9 -->|read_db| 11;\n  12[\"Merqury\"];\n  2 -->|output| 12;\n  9 -->|read_db| 12;\n"
     }
   ],

diff --git a/api/topics/assembly/tutorials/assembly-with-preprocessing/slides.json b/api/topics/assembly/tutorials/assembly-with-preprocessing/slides.json
@@ -115,7 +115,7 @@
       "name": "assembly_with_preprocessing",
       "title": "assembly_with_preprocessing",
       "test_results": null,
-      "modified": "2023-12-16 00:10:02 +0000",
+      "modified": "2023-12-17 00:10:44 +0000",
       "mermaid": "flowchart TD\n  0[\"Input dataset collection\"];\n  1[\"Input dataset collection\"];\n  10[\"Samtools fastx\"];\n  7 -->|outputsam| 10;\n  11[\"Samtools fastx\"];\n  9 -->|outputsam| 11;\n  12[\"Collapse Collection\"];\n  10 -->|nonspecific| 12;\n  13[\"Zip Collection\"];\n  11 -->|forward| 13;\n  11 -->|reverse| 13;\n  14[\"Collapse Collection\"];\n  11 -->|forward| 14;\n  15[\"Collapse Collection\"];\n  11 -->|reverse| 15;\n  16[\"seqtk_sample\"];\n  14 -->|output| 16;\n  17[\"seqtk_sample\"];\n  15 -->|output| 17;\n  18[\"Create assemblies with Unicycler\"];\n  12 -->|output| 18;\n  16 -->|default| 18;\n  17 -->|default| 18;\n  19[\"Bandage Info\"];\n  18 -->|assembly_graph| 19;\n  2[\"fastp\"];\n  0 -->|output| 2;\n  20[\"Filter sequences by length\"];\n  18 -->|assembly| 20;\n  21[\"Bandage Image\"];\n  18 -->|assembly_graph| 21;\n  3[\"NanoPlot\"];\n  1 -->|output| 3;\n  4[\"Map with minimap2\"];\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  2 -->|report_json| 5;\n  6[\"Bowtie2\"];\n  2 -->|output_paired_coll| 6;\n  7[\"Samtools view\"];\n  4 -->|alignment_output| 7;\n  8[\"Samtools stats\"];\n  4 -->|alignment_output| 8;\n  9[\"Samtools view\"];\n  6 -->|output| 9;\n"
     },
     {
@@ -133,7 +133,7 @@
       "name": "assembly_with_preprocessing_and_sra_download",
       "title": "assembly_with_preprocessing_and_sra_download",
       "test_results": null,
-      "modified": "2023-12-16 00:10:02 +0000",
+      "modified": "2023-12-17 00:10:44 +0000",
       "mermaid": "flowchart TD\n  0[\"Input dataset\"];\n  1[\"Input dataset\"];\n  10[\"Samtools stats\"];\n  6 -->|alignment_output| 10;\n  11[\"Samtools view\"];\n  8 -->|output| 11;\n  12[\"Samtools fastx\"];\n  9 -->|outputsam| 12;\n  13[\"Samtools fastx\"];\n  11 -->|outputsam| 13;\n  14[\"Collapse Collection\"];\n  12 -->|nonspecific| 14;\n  15[\"Zip Collection\"];\n  13 -->|forward| 15;\n  13 -->|reverse| 15;\n  16[\"Collapse Collection\"];\n  13 -->|forward| 16;\n  17[\"Collapse Collection\"];\n  13 -->|reverse| 17;\n  18[\"seqtk_sample\"];\n  16 -->|output| 18;\n  19[\"seqtk_sample\"];\n  17 -->|output| 19;\n  2[\"Faster Download and Extract Reads in FASTQ\"];\n  0 -->|output| 2;\n  20[\"Create assemblies with Unicycler\"];\n  14 -->|output| 20;\n  18 -->|default| 20;\n  19 -->|default| 20;\n  21[\"Bandage Info\"];\n  20 -->|assembly_graph| 21;\n  22[\"Bandage Image\"];\n  20 -->|assembly_graph| 22;\n  23[\"Filter sequences by length\"];\n  20 -->|assembly| 23;\n  3[\"Faster Download and Extract Reads in FASTQ\"];\n  1 -->|output| 3;\n  4[\"fastp\"];\n  2 -->|list_paired| 4;\n  5[\"NanoPlot\"];\n  3 -->|output_collection| 5;\n  6[\"Map with minimap2\"];\n  3 -->|output_collection| 6;\n  7[\"MultiQC\"];\n  4 -->|report_json| 7;\n  8[\"Bowtie2\"];\n  4 -->|output_paired_coll| 8;\n  9[\"Samtools view\"];\n  6 -->|alignment_output| 9;\n"
     }
   ],

diff --git a/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json b/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json
@@ -124,7 +124,7 @@
       "name": "assembly_with_preprocessing",
       "title": "assembly_with_preprocessing",
       "test_results": null,
-      "modified": "2023-12-16 00:10:02 +0000",
+      "modified": "2023-12-17 00:10:44 +0000",
       "mermaid": "flowchart TD\n  0[\"Input dataset collection\"];\n  1[\"Input dataset collection\"];\n  10[\"Samtools fastx\"];\n  7 -->|outputsam| 10;\n  11[\"Samtools fastx\"];\n  9 -->|outputsam| 11;\n  12[\"Collapse Collection\"];\n  10 -->|nonspecific| 12;\n  13[\"Zip Collection\"];\n  11 -->|forward| 13;\n  11 -->|reverse| 13;\n  14[\"Collapse Collection\"];\n  11 -->|forward| 14;\n  15[\"Collapse Collection\"];\n  11 -->|reverse| 15;\n  16[\"seqtk_sample\"];\n  14 -->|output| 16;\n  17[\"seqtk_sample\"];\n  15 -->|output| 17;\n  18[\"Create assemblies with Unicycler\"];\n  12 -->|output| 18;\n  16 -->|default| 18;\n  17 -->|default| 18;\n  19[\"Bandage Info\"];\n  18 -->|assembly_graph| 19;\n  2[\"fastp\"];\n  0 -->|output| 2;\n  20[\"Filter sequences by length\"];\n  18 -->|assembly| 20;\n  21[\"Bandage Image\"];\n  18 -->|assembly_graph| 21;\n  3[\"NanoPlot\"];\n  1 -->|output| 3;\n  4[\"Map with minimap2\"];\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  2 -->|report_json| 5;\n  6[\"Bowtie2\"];\n  2 -->|output_paired_coll| 6;\n  7[\"Samtools view\"];\n  4 -->|alignment_output| 7;\n  8[\"Samtools stats\"];\n  4 -->|alignment_output| 8;\n  9[\"Samtools view\"];\n  6 -->|output| 9;\n"
     },
     {
@@ -142,7 +142,7 @@
       "name": "assembly_with_preprocessing_and_sra_download",
       "title": "assembly_with_preprocessing_and_sra_download",
       "test_results": null,
-      "modified": "2023-12-16 00:10:02 +0000",
+      "modified": "2023-12-17 00:10:44 +0000",
       "mermaid": "flowchart TD\n  0[\"Input dataset\"];\n  1[\"Input dataset\"];\n  10[\"Samtools stats\"];\n  6 -->|alignment_output| 10;\n  11[\"Samtools view\"];\n  8 -->|output| 11;\n  12[\"Samtools fastx\"];\n  9 -->|outputsam| 12;\n  13[\"Samtools fastx\"];\n  11 -->|outputsam| 13;\n  14[\"Collapse Collection\"];\n  12 -->|nonspecific| 14;\n  15[\"Zip Collection\"];\n  13 -->|forward| 15;\n  13 -->|reverse| 15;\n  16[\"Collapse Collection\"];\n  13 -->|forward| 16;\n  17[\"Collapse Collection\"];\n  13 -->|reverse| 17;\n  18[\"seqtk_sample\"];\n  16 -->|output| 18;\n  19[\"seqtk_sample\"];\n  17 -->|output| 19;\n  2[\"Faster Download and Extract Reads in FASTQ\"];\n  0 -->|output| 2;\n  20[\"Create assemblies with Unicycler\"];\n  14 -->|output| 20;\n  18 -->|default| 20;\n  19 -->|default| 20;\n  21[\"Bandage Info\"];\n  20 -->|assembly_graph| 21;\n  22[\"Bandage Image\"];\n  20 -->|assembly_graph| 22;\n  23[\"Filter sequences by length\"];\n  20 -->|assembly| 23;\n  3[\"Faster Download and Extract Reads in FASTQ\"];\n  1 -->|output| 3;\n  4[\"fastp\"];\n  2 -->|list_paired| 4;\n  5[\"NanoPlot\"];\n  3 -->|output_collection| 5;\n  6[\"Map with minimap2\"];\n  3 -->|output_collection| 6;\n  7[\"MultiQC\"];\n  4 -->|report_json| 7;\n  8[\"Bowtie2\"];\n  4 -->|output_paired_coll| 8;\n  9[\"Samtools view\"];\n  6 -->|alignment_output| 9;\n"
     }
   ],

diff --git a/api/topics/assembly/tutorials/chloroplast-assembly/tutorial.json b/api/topics/assembly/tutorials/chloroplast-assembly/tutorial.json
@@ -94,7 +94,7 @@
       "name": "Chloroplast-genome-assembly-and-annotation",
       "title": "Chloroplast-genome-assembly-and-annotation",
       "test_results": null,
-      "modified": "2023-12-16 00:10:02 +0000",
+      "modified": "2023-12-17 00:10:44 +0000",
       "mermaid": "flowchart TD\n  0[\"Input dataset\"];\n  1[\"Input dataset\"];\n  2[\"Input dataset\"];\n  3[\"Input dataset\"];\n  4[\"Flye assembly\"];\n  1 -->|output| 4;\n  5[\"NanoPlot\"];\n  1 -->|output| 5;\n  6[\"Map with BWA-MEM\"];\n  0 -->|output| 6;\n  4 -->|consensus| 6;\n  7[\"Fasta Statistics\"];\n  4 -->|consensus| 7;\n  8[\"Bandage Info\"];\n  4 -->|assembly_gfa| 8;\n  9[\"Bandage Image\"];\n  4 -->|assembly_gfa| 9;\n  10[\"pilon\"];\n  6 -->|bam_output| 10;\n  4 -->|consensus| 10;\n  11[\"Fasta Statistics\"];\n  10 -->|output_fasta| 11;\n  12[\"Map with BWA-MEM\"];\n  2 -->|output| 12;\n  10 -->|output_fasta| 12;\n  13[\"Map with BWA-MEM\"];\n  3 -->|output| 13;\n  10 -->|output_fasta| 13;\n  14[\"Prokka\"];\n  10 -->|output_fasta| 14;\n  15[\"JBrowse\"];\n  10 -->|output_fasta| 15;\n  12 -->|bam_output| 15;\n  13 -->|bam_output| 15;\n  16[\"JBrowse\"];\n  10 -->|output_fasta| 16;\n  14 -->|out_gff| 16;\n"
     }
   ],

diff --git a/api/topics/assembly/tutorials/debruijn-graph-assembly/slides.json b/api/topics/assembly/tutorials/debruijn-graph-assembly/slides.json
@@ -54,7 +54,7 @@
       "name": "Debruijn Graph",
       "title": "Debruijn Graph",
       "test_results": null,
-      "modified": "2023-12-16 00:10:02 +0000",
+      "modified": "2023-12-17 00:10:44 +0000",
       "mermaid": "flowchart TD\n  0[\"Input dataset\"];\n  1[\"Input dataset\"];\n  2[\"VelvetOptimiser\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"SPAdes\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Fasta Statistics\"];\n  2 -->|contigs| 4;\n  5[\"Fasta Statistics\"];\n  3 -->|out_contigs| 5;\n"
     }
   ],

diff --git a/api/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.json b/api/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.json
@@ -115,7 +115,7 @@
       "name": "Debruijn Graph",
       "title": "Debruijn Graph",
       "test_results": null,
-      "modified": "2023-12-16 00:10:02 +0000",
+      "modified": "2023-12-17 00:10:44 +0000",
       "mermaid": "flowchart TD\n  0[\"Input dataset\"];\n  1[\"Input dataset\"];\n  2[\"VelvetOptimiser\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"SPAdes\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Fasta Statistics\"];\n  2 -->|contigs| 4;\n  5[\"Fasta Statistics\"];\n  3 -->|out_contigs| 5;\n"
     }
   ],

diff --git a/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json b/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json
@@ -107,7 +107,7 @@
       "name": "Ecoli Comparison",
       "title": "Ecoli Comparison",
       "test_results": null,
-      "modified": "2023-12-16 00:10:02 +0000",
+      "modified": "2023-12-17 00:10:44 +0000",
       "mermaid": "flowchart TD\n  0[\"Input dataset\"];\n  1[\"Input dataset\"];\n  10[\"Collapse Collection\"];\n  6 -->|output| 10;\n  11[\"Text transformation\"];\n  7 -->|output| 11;\n  12[\"Add column\"];\n  8 -->|out_file1| 12;\n  13[\"LASTZ\"];\n  9 -->|output| 13;\n  3 -->|output| 13;\n  14[\"random_lines1\"];\n  10 -->|output| 14;\n  15[\"Filter\"];\n  10 -->|output| 15;\n  16[\"Search in textfiles\"];\n  11 -->|output| 16;\n  17[\"Concatenate datasets\"];\n  11 -->|output| 17;\n  9 -->|output| 17;\n  18[\"Cut\"];\n  12 -->|out_file1| 18;\n  19[\"Text transformation\"];\n  13 -->|output| 19;\n  2[\"Input dataset collection\"];\n  20[\"Datamash\"];\n  15 -->|out_file1| 20;\n  21[\"Compute sequence length\"];\n  17 -->|out_file1| 21;\n  22[\"Collapse Collection\"];\n  18 -->|out_file1| 22;\n  23[\"Merge Columns\"];\n  19 -->|output| 23;\n  24[\"Select\"];\n  20 -->|out_file| 24;\n  25[\"Sort\"];\n  21 -->|output| 25;\n  26[\"Collapse Collection\"];\n  23 -->|out_file1| 26;\n  27[\"Cut\"];\n  26 -->|output| 27;\n  28[\"Cut\"];\n  26 -->|output| 28;\n  29[\"Concatenate datasets\"];\n  27 -->|out_file1| 29;\n  28 -->|out_file1| 29;\n  3[\"Input dataset collection\"];\n  30[\"SortBED\"];\n  29 -->|out_file1| 30;\n  31[\"ComplementBed\"];\n  25 -->|outfile| 31;\n  30 -->|output| 31;\n  32[\"Filter\"];\n  31 -->|output| 32;\n  33[\"Filter\"];\n  32 -->|out_file1| 33;\n  34[\"Intersect intervals\"];\n  33 -->|out_file1| 34;\n  22 -->|output| 34;\n  35[\"Join two Datasets\"];\n  34 -->|output| 35;\n  1 -->|output| 35;\n  4[\"Input dataset collection\"];\n  5[\"Filter sequences by length\"];\n  0 -->|output| 5;\n  6[\"LASTZ\"];\n  2 -->|output| 6;\n  0 -->|output| 6;\n  7[\"Collapse Collection\"];\n  3 -->|output| 7;\n  8[\"Select\"];\n  4 -->|output| 8;\n  9[\"Text transformation\"];\n  5 -->|output| 9;\n"
     }
   ],