Fixed 183,184,179,178

Plant-Food-Research-Open · Dec 11, 2024 · 1e7ab55 · 1e7ab55
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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. [email protected]
+
+### `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/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 +1,23 @@
 <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>
+    <ul>
+      <li>
+        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.
+      </li>
+    </ul>
+
+  </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 +1,32 @@
 <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>
+    <ul>
+      <li>
+        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.
+      </li>
+    </ul>
+
+  </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_plotsr/synteny_plotsr.html b/bin/report_modules/templates/synteny_plotsr/synteny_plotsr.html
@@ -31,6 +31,15 @@
         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>
+    <ul>
+      <li>
+        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.
+      </li>
+    </ul>
+
   </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 }

diff --git a/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf b/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf
@@ -2,8 +2,6 @@
 // Subworkflow with functionality specific to the plant-food-research-open/assemblyqc pipeline
 //
 
-import groovy.json.JsonOutput
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS
@@ -81,12 +79,12 @@ workflow PIPELINE_INITIALISATION {
                                             | collect
                                             | map { tags -> validateInputTags( tags ) }
                                             | combine ( ch_input.map { row -> [ row ] } )
-                                            | map { result, row -> row }
+                                            | map { _result, row -> row }
 
     ch_hic_reads                            = ! params.hic
                                             ? Channel.empty()
                                             : (
-                                                "$params.hic".find(/.*[\/].*\.(fastq|fq)\.gz/)
+                                                "$params.hic".find(/\S+\{1,2\}[\w\.]*\.f(ast)?q\.gz/)
                                                 ? Channel.fromFilePairs(params.hic, checkIfExists: true)
                                                 : Channel.of( [ params.hic, 'is_sra' ] )
                                             )
@@ -105,7 +103,7 @@ workflow PIPELINE_INITIALISATION {
                                             | collect
                                             | map { tags -> validateXrefAssemblies( tags ) }
                                             | combine ( ch_xref_assembly.map { row -> [ row ] } )
-                                            | map { result, row -> row }
+                                            | map { _result, row -> row }
                                             | map { tag, fa, labels ->
                                                 [ tag, file(fa, checkIfExists: true), file(labels, checkIfExists: true) ]
                                             }
@@ -275,7 +273,7 @@ def validateInputTags(assemblyTags) {
     assemblyTags.each { tag ->
         tagCounts[tag] = tagCounts.containsKey(tag) ? tagCounts[tag] + 1 : 1
     }
-    def repeatedTags = tagCounts.findAll { key, count -> count > 1 }.collect { key, count -> key }
+    def repeatedTags = tagCounts.findAll { _key, count -> count > 1 }.collect { key, _count -> key }
 
     if (repeatedTags.size() > 0) {
         error("Please check input assemblysheet -> Multiple assemblies have the same tags!: ${repeatedTags}")
@@ -290,7 +288,7 @@ def validateXrefAssemblies(xrefTags) {
     xrefTags.each { tag ->
         tagCounts[tag] = tagCounts.containsKey(tag) ? tagCounts[tag] + 1 : 1
     }
-    def repeatedTags = tagCounts.findAll { key, count -> count > 1 }.collect { key, count -> key }
+    def repeatedTags = tagCounts.findAll { _key, count -> count > 1 }.collect { key, _count -> key }
 
     if (repeatedTags.size() > 0) {
         error("Please check synteny_xref_assemblies -> Multiple xref assemblies have the same tags!: ${repeatedTags}")
@@ -300,7 +298,7 @@ def validateXrefAssemblies(xrefTags) {
 }
 
 def jsonifyParams(params) {
-    return JsonOutput.toJson(params).toString()
+    return groovy.json.JsonOutput.toJson(params).toString()
 }
 
 def jsonifySummaryParams(params) {
@@ -312,7 +310,7 @@ def jsonifySummaryParams(params) {
         }
     }
 
-    return JsonOutput.toJson(summary).toString()
+    return groovy.json.JsonOutput.toJson(summary).toString()
 }
 
 def extractReadsTuple(tag, reads_1, reads_2) {