Merge pull request #185 from Plant-Food-Research-Open/patch/184

Patched 183,184,179,178 for 2.2.1
Plant-Food-Research-Open · Dec 11, 2024 · 39eb040 · 39eb040
2 parents 0141925 + 0439cbf
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diff --git a/.nf-core.yml b/.nf-core.yml
@@ -46,5 +46,5 @@ template:
     - igenomes
     - multiqc
     - fastqc
-  version: 2.2.0dev
+  version: 2.2.1
 update: null
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,25 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v2.2.1 - [11-Dec-2024]
+
+### `Added`
+
+1. Added notes on HTTP(s) server on the HiC page and on the need to move dynamically loaded content when moving the report's HTML file [#183](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/183)
+
+### `Fixed`
+
+1. Fixed an issue where PLOTSR crashed due to a mismatch in the ordering of `syri.out` files when `synteny_plotsr_assembly_order` was not specified [#184](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/184)
+2. Fixed an issue where a path to HiC FastQ file pairs from the current directory were considered a SRR ID [#179](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/179)
+3. Fixed edges and input/output arrows in the flowchart [#178](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/178)
+
+### `Dependencies`
+
+1. Nextflow!>=24.04.2
+2. nf-schema@2.1.1
+
+### `Deprecated`
+
 ## v2.2.0 - [05-Nov-2024]
 
 ### `Added`

diff --git a/CITATION.cff b/CITATION.cff
@@ -25,7 +25,7 @@ authors:
   - family-names: "Deng"
     given-names: "Cecilia"
 title: "AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality"
-version: 2.2.0
+version: 2.2.1
 date-released: 2024-07-30
 url: "https://github.com/Plant-Food-Research-Open/assemblyqc"
 doi: 10.1093/bioinformatics/btae477
diff --git a/bin/report_modules/parsers/synteny_parser.py b/bin/report_modules/parsers/synteny_parser.py
@@ -147,9 +147,12 @@ def parse_synteny_plotsr(folder_name="synteny_outputs"):
             "error_message": (
                 None
                 if error_comparisons == []
-                else "<b>Note:</b> Syri failed to detect structural rearrangements for following comparisons: "
+                else '<b style="color: red;">Error:</b> Syri failed to detect structural rearrangements for following comparisons: '
                 + ", ".join(
-                    [f"{target} with reference to {ref}" for (target, ref) in error_comparisons]
+                    [
+                        f"{target} with reference to {ref}"
+                        for (target, ref) in error_comparisons
+                    ]
                 )
                 + '. This may be due to known Syri limitations. See: <a href="https://github.com/schneebergerlab/syri/tree/ebd0f832e0df33398306f1b65f86801090c1ed49#current-limitations" target="_blank">GitHub/Syri/Limitations</a>'
             ),

diff --git a/bin/report_modules/templates/header.html b/bin/report_modules/templates/header.html
@@ -136,6 +136,7 @@
             width: 90%;
             min-width: 700px;
             margin: auto;
+            padding-bottom: 16px;
         }
 
         .dropdown select {

diff --git a/bin/report_modules/templates/hic/hic.html b/bin/report_modules/templates/hic/hic.html
@@ -8,38 +8,57 @@
     <p class="section-para"><b>References:</b></p>
 
     <p class="section-para">
-      <b>fastp</b> Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics,
+      <b>fastp</b> Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor,
+      Bioinformatics,
       Volume 34, Issue 17, September 2018, Pages i884–i890, <a href="https://doi.org/10.1093/bioinformatics/bty560"
         target="_blank">10.1093/bioinformatics/bty560</a>
     </p>
 
     <p class="section-para">
-      <b>BWA</b> Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint <a
-        href="https://arxiv.org/abs/1303.3997" target="_blank">arXiv: 1303.3997</a>.
+      <b>BWA</b> Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv
+      preprint <a href="https://arxiv.org/abs/1303.3997" target="_blank">arXiv: 1303.3997</a>.
     </p>
 
     <p class="section-para">
-      <b>SAMBLASTER</b> Gregory G. Faust, Ira M. Hall, SAMBLASTER: fast duplicate marking and structural variant read extraction,
+      <b>SAMBLASTER</b> Gregory G. Faust, Ira M. Hall, SAMBLASTER: fast duplicate marking and structural variant read
+      extraction,
       Bioinformatics, Volume 30, Issue 17, September 2014, Pages 2503–2505, <a
         href="https://doi.org/10.1093/bioinformatics/btu314" target="_blank">10.1093/bioinformatics/btu314</a>
     </p>
 
     <p class="section-para">
-      <b>SAMtools</b> Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham,
+      <b>SAMtools</b> Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard,
+      Andrew Whitwham,
       Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li, Twelve years of SAMtools and BCFtools, GigaScience,
       Volume
       10, Issue 2, February 2021, giab008, <a href="https://doi.org/10.1093/gigascience/giab008"
         target="_blank">10.1093/gigascience/giab008</a>
     </p>
 
     <p class="section-para">
-      <b>Juicebox.js</b> Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL. Juicebox.js Provides a
+      <b>Juicebox.js</b> Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL. Juicebox.js Provides
+      a
       Cloud-Based Visualization System for Hi-C Data. Cell Syst. 2018 Feb 28;6(2):256-258.e1.
       <a href="https://doi.org/10.1016/j.cels.2018.01.001" target="_blank">10.1016/j.cels.2018.01.001</a>. Epub
       2018 Feb 7. PMID: 29428417; PMCID: PMC6047755.
     </p>
 
     <p class="section-para"><b>Version: {{ all_stats_dicts['VERSIONS']['JUICEBOX_JS'] }}</b></p>
+
+    <p class="section-para"><b>Notes:</b></p>
+    <ul>
+      <li>
+        The Hi-C contact map is only loaded when the report is opened through a HTTP(s) server and all the necessary
+        permissions are in place. The contact map '.hic' file is stored in the 'hic' folder under the output directory.
+        It can be visualized with <a href="https://github.com/aidenlab/Juicebox/wiki/Download">Juicebox</a>.
+      </li>
+      <li>
+        This report dynamically loads content from the 'hic' folder under the output directory including '*.hic',
+        '*.html', 'bedpe/' and 'hicqc/'. These files and folders should also be moved when moving the report's HTML
+        file.
+      </li>
+    </ul>
   </div>
+
   {% include 'hic/dropdown.html' %} {% include 'hic/report_contents.html' %}
 </div>
diff --git a/bin/report_modules/templates/kraken2/kraken2.html b/bin/report_modules/templates/kraken2/kraken2.html
@@ -1,14 +1,19 @@
 <div id="KRAKEN2" class="tabcontent" style="display: none">
-    <div class="section-para-wrapper">
-        <p class="section-para">
-            Kraken2 assigns taxonomic labels to sequencing reads for metagenomics projects.
-        </p>
-        <p class="section-para"><b>Reference:</b></p>
-        <p class="section-para">
-            Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019).
-            <a href="https://doi.org/10.1186/s13059-019-1891-0" target="_blank">10.1186/s13059-019-1891-0</a>
-        </p>
-        <p class="section-para"><b>Version: {{ all_stats_dicts['VERSIONS']['KRAKEN2']['kraken2'] }}</b></p>
-    </div>
-    {% include 'kraken2/dropdown.html' %} {% include 'kraken2/report_contents.html' %}
+  <div class="section-para-wrapper">
+    <p class="section-para">
+      Kraken2 assigns taxonomic labels to sequencing reads for metagenomics projects.
+    </p>
+    <p class="section-para"><b>Reference:</b></p>
+    <p class="section-para">
+      Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019).
+      <a href="https://doi.org/10.1186/s13059-019-1891-0" target="_blank">10.1186/s13059-019-1891-0</a>
+    </p>
+    <p class="section-para"><b>Version: {{ all_stats_dicts['VERSIONS']['KRAKEN2']['kraken2'] }}</b></p>
+
+    <p class="section-para"><b>Note:</b></p>
+    <p class="section-para">This report dynamically loads '*.kraken2.krona.html' files from the 'kraken2' folder under
+      the output directory. These files should also be moved when moving the report's HTML file.</p>
+
+  </div>
+  {% include 'kraken2/dropdown.html' %} {% include 'kraken2/report_contents.html' %}
 </div>
diff --git a/bin/report_modules/templates/ncbi_fcs_gx/ncbi_fcs_gx.html b/bin/report_modules/templates/ncbi_fcs_gx/ncbi_fcs_gx.html
@@ -1,23 +1,27 @@
 <div id="NCBI_FCS_GX" class="tabcontent" style="display: none">
-    <div class="section-para-wrapper">
-        <p class="section-para">FCS-GX detects contamination from foreign organisms in genome sequences.</p>
-        <p class="section-para"><b>Reference:</b></p>
-        <p class="section-para">
-            Alexander Astashyn, Eric S Tvedte, Deacon Sweeney, Victor Sapojnikov, Nathan Bouk, Victor Joukov, Eyal
-            Mozes, Pooja K Strope, Pape M Sylla, Lukas Wagner, Shelby L Bidwell, Karen Clark, Emily W Davis, Brian
-            Smith-White, Wratko Hlavina, Kim D Pruitt, Valerie A Schneider, Terence D Murphy bioRxiv 2023.06.02.543519;
-            doi:
-            <a href="https://doi.org/10.1101/2023.06.02.543519" target="_blank">10.1101/2023.06.02.543519</a>, GitHub:
-            <a href="https://github.com/ncbi/fcs" target="_blank">https://github.com/ncbi/fcs</a>
-        </p>
-        <p class="section-para">
-            <b>Version: {{ all_stats_dicts['VERSIONS']['NCBI_FCS_GX_SCREEN_SAMPLES']['fcs_gx'] }}</b>
-        </p>
-        <p class="section-para">
-            <b>DB Version: {{ all_stats_dicts['NCBI_FCS_GX'][0]['report_meta_data'][1]['db']['build-date'] }}</b>
-        </p>
-    </div>
-    {% include 'ncbi_fcs_gx/dropdown.html' %}
-    {% include 'ncbi_fcs_gx/summary_contents.html' %}
-    {% include 'ncbi_fcs_gx/report_contents.html' %}
+  <div class="section-para-wrapper">
+    <p class="section-para">FCS-GX detects contamination from foreign organisms in genome sequences.</p>
+    <p class="section-para"><b>Reference:</b></p>
+    <p class="section-para">
+      Alexander Astashyn, Eric S Tvedte, Deacon Sweeney, Victor Sapojnikov, Nathan Bouk, Victor Joukov, Eyal
+      Mozes, Pooja K Strope, Pape M Sylla, Lukas Wagner, Shelby L Bidwell, Karen Clark, Emily W Davis, Brian
+      Smith-White, Wratko Hlavina, Kim D Pruitt, Valerie A Schneider, Terence D Murphy bioRxiv 2023.06.02.543519;
+      doi:
+      <a href="https://doi.org/10.1101/2023.06.02.543519" target="_blank">10.1101/2023.06.02.543519</a>, GitHub:
+      <a href="https://github.com/ncbi/fcs" target="_blank">https://github.com/ncbi/fcs</a>
+    </p>
+    <p class="section-para">
+      <b>Version: {{ all_stats_dicts['VERSIONS']['NCBI_FCS_GX_SCREEN_SAMPLES']['fcs_gx'] }}</b>
+    </p>
+    <p class="section-para">
+      <b>DB Version: {{ all_stats_dicts['NCBI_FCS_GX'][0]['report_meta_data'][1]['db']['build-date'] }}</b>
+    </p>
+
+    <p class="section-para"><b>Note:</b></p>
+    <p class="section-para">This report dynamically loads '*.fcs.gx.krona.html' files from the 'ncbi_fcs_gx' folder under the output
+      directory. These files should also be moved when moving the report's HTML file.</p>
+  </div>
+  {% include 'ncbi_fcs_gx/dropdown.html' %}
+  {% include 'ncbi_fcs_gx/summary_contents.html' %}
+  {% include 'ncbi_fcs_gx/report_contents.html' %}
 </div>
diff --git a/bin/report_modules/templates/synteny_circos/synteny_circos.html b/bin/report_modules/templates/synteny_circos/synteny_circos.html
@@ -1,39 +1,42 @@
 <div id="SYNTENY_CIRCOS" class="tabcontent" style="display: none">
-    <div class="section-para-wrapper">
-        <p class="section-para">
-            Circos facilitates the identification and analysis of similarities and differences arising from comparisons
-            of genomes. The genome-wide alignments are performed with MUMMER.
-        </p>
-        <p class="section-para"><b>References:</b></p>
-        <p class="section-para">
-            Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., ... & Marra, M. A. (2009).
-            Circos: an information aesthetic for comparative genomics. Genome research, 19(9), 1639-1645.
-            <a href="https://doi.org/10.1101/gr.092759.109" target="_blank">10.1101/gr.092759.109</a>
-        </p>
-        <p class="section-para">
-            Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome
-            alignment system. PLoS Comput Biol. 2018 Jan 26;14(1):e1005944.
-            <a href="https://doi.org/10.1371/journal.pcbi.1005944" target="_blank">10.1371/journal.pcbi.1005944</a>
-        </p>
-        <p class="section-para">
-            <b
-                >Versions: {{ all_stats_dicts['VERSIONS']['CIRCOS']['circos'] }} (CIRCOS), {{
-                all_stats_dicts['VERSIONS']['MUMMER']['nucmer'] }} (MUMMER)</b
-            >
-        </p>
-        <p class="section-para"><b>Notes:</b></p>
-        <ul>
-          <li>
-            Alignments within a distance of {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_max_gap'] }}bp have been
-            bundled together.
-          </li>
-          <li>
-            After bundling, any bundle smaller than {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_min_bundle_size'] }}bp has been filtered out.
-          </li>
-          <li>
-            The sequence labels shown on the plot are based on the labelling file provided to the pipeline. These labels may or may not be same as the sequence IDs in the corresponding FASTA files.
-          </li>
-        </ul>
-    </div>
-    {% include 'synteny_circos/dropdown.html' %} {% include 'synteny_circos/report_contents.html' %}
+  <div class="section-para-wrapper">
+    <p class="section-para">
+      Circos facilitates the identification and analysis of similarities and differences arising from comparisons
+      of genomes. The genome-wide alignments are performed with MUMMER.
+    </p>
+    <p class="section-para"><b>References:</b></p>
+    <p class="section-para">
+      Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., ... & Marra, M. A. (2009).
+      Circos: an information aesthetic for comparative genomics. Genome research, 19(9), 1639-1645.
+      <a href="https://doi.org/10.1101/gr.092759.109" target="_blank">10.1101/gr.092759.109</a>
+    </p>
+    <p class="section-para">
+      Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome
+      alignment system. PLoS Comput Biol. 2018 Jan 26;14(1):e1005944.
+      <a href="https://doi.org/10.1371/journal.pcbi.1005944" target="_blank">10.1371/journal.pcbi.1005944</a>
+    </p>
+    <p class="section-para">
+      <b>Versions: {{ all_stats_dicts['VERSIONS']['CIRCOS']['circos'] }} (CIRCOS), {{
+        all_stats_dicts['VERSIONS']['MUMMER']['nucmer'] }} (MUMMER)</b>
+    </p>
+
+    <p class="section-para"><b>Notes:</b></p>
+    <ul>
+      <li>
+        Alignments within a distance of {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_max_gap'] }}bp have been
+        bundled together.
+      </li>
+      <li>
+        After bundling, any bundle smaller than {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_min_bundle_size'] }}bp
+        has been filtered out.
+      </li>
+      <li>
+        The sequence labels shown on the plot are based on the labelling file provided to the pipeline. These labels may
+        or may not be same as the sequence IDs in the corresponding FASTA files.
+      </li>
+    </ul>
+
+  </div>
+
+  {% include 'synteny_circos/dropdown.html' %} {% include 'synteny_circos/report_contents.html' %}
 </div>
diff --git a/bin/report_modules/templates/synteny_dotplot/synteny_dotplot.html b/bin/report_modules/templates/synteny_dotplot/synteny_dotplot.html
@@ -10,14 +10,16 @@
     <p class="section-para">
       <b>Version: {{ all_stats_dicts['VERSIONS']['MUMMER']['nucmer'] }} (MUMMER)</b>
     </p>
+
     <p class="section-para"><b>Notes:</b></p>
     <ul>
       <li>
         Alignments within a distance of {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_max_gap'] }}bp have been
         bundled together.
       </li>
       <li>
-        After bundling, any bundle smaller than {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_min_bundle_size'] }}bp has
+        After bundling, any bundle smaller than {{ all_stats_dicts['PARAMS_DICT']['synteny_mummer_min_bundle_size'] }}bp
+        has
         been filtered out.
       </li>
       <li>
@@ -26,5 +28,6 @@
       </li>
     </ul>
   </div>
+
   {% include 'synteny_dotplot/dropdown.html' %} {% include 'synteny_dotplot/report_contents.html' %}
 </div>
diff --git a/bin/report_modules/templates/synteny_plotsr/synteny_plotsr.html b/bin/report_modules/templates/synteny_plotsr/synteny_plotsr.html
@@ -31,6 +31,11 @@
         all_stats_dicts['VERSIONS']['SYRI']['syri'] }} (SYRI), {{
         all_stats_dicts['VERSIONS']['MINIMAP2_ALIGN']['minimap2'] }} (MINIMAP2)</b>
     </p>
+
+    <p class="section-para"><b>Note:</b></p>
+    <p>This report dynamically loads '*.on.*.all/' folders from the 'synteny' folder under the output directory. These
+      folders should also be moved when moving the report's HTML file.</p>
+
   </div>
   {% include 'synteny_plotsr/report_contents.html' %}
 </div>
diff --git a/docs/images/assemblyqc.png b/docs/images/assemblyqc.png
diff --git a/nextflow.config b/nextflow.config
@@ -274,7 +274,7 @@ manifest {
     description     = """A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '2.2.0'
+    version         = '2.2.1'
     doi             = 'https://doi.org/10.1093/bioinformatics/btae477'
 }
 

diff --git a/subworkflows/local/fasta_synteny.nf b/subworkflows/local/fasta_synteny.nf
@@ -344,7 +344,7 @@ workflow FASTA_SYNTENY {
                                         | map { meta, syri, fastas ->
                                             def fasta_list          = fastas.flatten()
                                             def syri_tags           = syri.collect { it.name.replace('syri.out', '').split(/\.on\./).toList() }.flatten().unique()
-                                            def proposed_order      = plotsr_assembly_order ? plotsr_assembly_order.tokenize(' ') : syri_tags.sort(false)
+                                            def proposed_order      = plotsr_assembly_order ? plotsr_assembly_order.tokenize(' ') : syri_tags.sort(false) { it.toUpperCase() }
 
                                             def available_tags      = []
                                             proposed_order.each { tag -> if ( tag in syri_tags ) available_tags << tag }