From 1e7ab55be5003809cedee86ed5e5fc89a6703159 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 11 Dec 2024 13:35:36 +1300 Subject: [PATCH 1/3] Fixed 183,184,179,178 --- .nf-core.yml | 2 +- CHANGELOG.md | 19 +++++++ CITATION.cff | 2 +- bin/report_modules/templates/hic/hic.html | 31 ++++++++--- .../templates/kraken2/kraken2.html | 33 +++++++----- .../templates/ncbi_fcs_gx/ncbi_fcs_gx.html | 51 ++++++++++-------- .../synteny_plotsr/synteny_plotsr.html | 9 ++++ docs/images/assemblyqc.png | Bin 581306 -> 590296 bytes nextflow.config | 2 +- subworkflows/local/fasta_synteny.nf | 2 +- .../utils_nfcore_assemblyqc_pipeline/main.nf | 16 +++--- 11 files changed, 115 insertions(+), 52 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index b62355dd..9ed7bfc3 100644 --- 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 index 1c5def16..c9effe79 100644 --- 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 index 18bb4b7d..2908aa72 100644 --- 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 index 2af561e7..eb8cffd8 100644 --- a/bin/report_modules/templates/hic/hic.html +++ b/bin/report_modules/templates/hic/hic.html @@ -8,24 +8,27 @@

References:

- fastp Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, + fastp 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, 10.1093/bioinformatics/bty560

- BWA Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv: 1303.3997. + BWA Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv + preprint arXiv: 1303.3997.

- SAMBLASTER Gregory G. Faust, Ira M. Hall, SAMBLASTER: fast duplicate marking and structural variant read extraction, + SAMBLASTER 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, 10.1093/bioinformatics/btu314

- SAMtools Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, + SAMtools 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,

- Juicebox.js Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL. Juicebox.js Provides a + Juicebox.js 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. 10.1016/j.cels.2018.01.001. Epub 2018 Feb 7. PMID: 29428417; PMCID: PMC6047755.

Version: {{ all_stats_dicts['VERSIONS']['JUICEBOX_JS'] }}

+ +

Notes:

+ + {% include 'hic/dropdown.html' %} {% include 'hic/report_contents.html' %} diff --git a/bin/report_modules/templates/kraken2/kraken2.html b/bin/report_modules/templates/kraken2/kraken2.html index 250eebf3..88ea2d3a 100644 --- a/bin/report_modules/templates/kraken2/kraken2.html +++ b/bin/report_modules/templates/kraken2/kraken2.html @@ -1,14 +1,23 @@ 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 index fecca37e..e53a7d28 100644 --- 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 @@ diff --git a/bin/report_modules/templates/synteny_plotsr/synteny_plotsr.html b/bin/report_modules/templates/synteny_plotsr/synteny_plotsr.html index 60060828..4c45b085 100644 --- 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)

+ +

Note:

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zP1=(cG#GlYUnqH;^2l)dWtDzE{SE4$-$=3s!~Z;kz98SVj6!YlOX|zeJ|JdL(l7}# z1=w3dWo00&WSI?99s-aw!pW&svr74#e*wbwAcA;l=}mP2FOs>!Q?Spx%N4{mTufX{ zQNW$n<{K~08YX{stB`ZO4JHB^kVO}f=Q9cd$`nol+pnk zYWXb+3cl=KO7Z@k9qzr4-)_k+J(K=_e0_H~m;Kwn@gXaFXJxOfN>)}#HrXpPGb - + {% include 'hic/dropdown.html' %} {% include 'hic/report_contents.html' %} diff --git a/bin/report_modules/templates/kraken2/kraken2.html b/bin/report_modules/templates/kraken2/kraken2.html index 88ea2d3a..f1c957e1 100644 --- a/bin/report_modules/templates/kraken2/kraken2.html +++ b/bin/report_modules/templates/kraken2/kraken2.html @@ -11,12 +11,8 @@

Version: {{ all_stats_dicts['VERSIONS']['KRAKEN2']['kraken2'] }}

Note:

-
    -
  • - 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. -
    • -
+

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.

{% include 'kraken2/dropdown.html' %} {% include 'kraken2/report_contents.html' %} 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 index e53a7d28..e302ed41 100644 --- a/bin/report_modules/templates/ncbi_fcs_gx/ncbi_fcs_gx.html +++ b/bin/report_modules/templates/ncbi_fcs_gx/ncbi_fcs_gx.html @@ -18,13 +18,8 @@

Note:

-
    -
  • - 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. -
    • -
- +

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.

{% include 'ncbi_fcs_gx/dropdown.html' %} {% include 'ncbi_fcs_gx/summary_contents.html' %} diff --git a/bin/report_modules/templates/synteny_circos/synteny_circos.html b/bin/report_modules/templates/synteny_circos/synteny_circos.html index d7547707..3d410d30 100644 --- a/bin/report_modules/templates/synteny_circos/synteny_circos.html +++ b/bin/report_modules/templates/synteny_circos/synteny_circos.html @@ -1,39 +1,42 @@ diff --git a/bin/report_modules/templates/synteny_dotplot/synteny_dotplot.html b/bin/report_modules/templates/synteny_dotplot/synteny_dotplot.html index 91e1bd83..0c38c11d 100644 --- a/bin/report_modules/templates/synteny_dotplot/synteny_dotplot.html +++ b/bin/report_modules/templates/synteny_dotplot/synteny_dotplot.html @@ -10,6 +10,7 @@

Version: {{ all_stats_dicts['VERSIONS']['MUMMER']['nucmer'] }} (MUMMER)

+

Notes:

  • @@ -17,7 +18,8 @@ bundled together.
  • - 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.
  • @@ -26,5 +28,6 @@
+ {% include 'synteny_dotplot/dropdown.html' %} {% include 'synteny_dotplot/report_contents.html' %} diff --git a/bin/report_modules/templates/synteny_plotsr/synteny_plotsr.html b/bin/report_modules/templates/synteny_plotsr/synteny_plotsr.html index 4c45b085..fb131ad1 100644 --- a/bin/report_modules/templates/synteny_plotsr/synteny_plotsr.html +++ b/bin/report_modules/templates/synteny_plotsr/synteny_plotsr.html @@ -33,12 +33,8 @@

Note:

-
    -
  • - 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. -
    • -
+

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.

{% include 'synteny_plotsr/report_contents.html' %} From 0439cbf2c8fc58fd94d058ca661665eb085a5ffc Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 11 Dec 2024 15:42:08 +1300 Subject: [PATCH 3/3] Updated snapshots --- tests/hicparam/main.nf.test.snap | 2 +- tests/invalid/main.nf.test.snap | 2 +- tests/minimal/main.nf.test.snap | 2 +- tests/noltr/main.nf.test.snap | 2 +- tests/orthofinder/main.nf.test.snap | 2 +- tests/stub/main.nf.test.snap | 2 +- tests/tiny/main.nf.test.snap | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/tests/hicparam/main.nf.test.snap b/tests/hicparam/main.nf.test.snap index db89beee..a6e53fcf 100644 --- a/tests/hicparam/main.nf.test.snap +++ b/tests/hicparam/main.nf.test.snap @@ -68,7 +68,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0" + "plant-food-research-open/assemblyqc": "v2.2.1" } }, "stable paths": [ diff --git a/tests/invalid/main.nf.test.snap b/tests/invalid/main.nf.test.snap index c29b15ad..92cfa7c1 100644 --- a/tests/invalid/main.nf.test.snap +++ b/tests/invalid/main.nf.test.snap @@ -35,7 +35,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0" + "plant-food-research-open/assemblyqc": "v2.2.1" } }, "stable paths": [ diff --git a/tests/minimal/main.nf.test.snap b/tests/minimal/main.nf.test.snap index 8e139a7e..dae5d99a 100644 --- a/tests/minimal/main.nf.test.snap +++ b/tests/minimal/main.nf.test.snap @@ -35,7 +35,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0" + "plant-food-research-open/assemblyqc": "v2.2.1" } }, "stable paths": [ diff --git a/tests/noltr/main.nf.test.snap b/tests/noltr/main.nf.test.snap index d1580b9d..56e4d7a8 100644 --- a/tests/noltr/main.nf.test.snap +++ b/tests/noltr/main.nf.test.snap @@ -50,7 +50,7 @@ "seqkit": "v2.8.0" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0" + "plant-food-research-open/assemblyqc": "v2.2.1" } }, "stable paths": [ diff --git a/tests/orthofinder/main.nf.test.snap b/tests/orthofinder/main.nf.test.snap index 4d34b485..6d457ac8 100644 --- a/tests/orthofinder/main.nf.test.snap +++ b/tests/orthofinder/main.nf.test.snap @@ -41,7 +41,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0" + "plant-food-research-open/assemblyqc": "v2.2.1" } }, "stable paths": [ diff --git a/tests/stub/main.nf.test.snap b/tests/stub/main.nf.test.snap index d2e05d4c..6d354a86 100644 --- a/tests/stub/main.nf.test.snap +++ b/tests/stub/main.nf.test.snap @@ -230,7 +230,7 @@ "untar": 1.34 }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0" + "plant-food-research-open/assemblyqc": "v2.2.1" } }, "stable paths": [ diff --git a/tests/tiny/main.nf.test.snap b/tests/tiny/main.nf.test.snap index b937e1d4..79ae24cf 100644 --- a/tests/tiny/main.nf.test.snap +++ b/tests/tiny/main.nf.test.snap @@ -29,7 +29,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0" + "plant-food-research-open/assemblyqc": "v2.2.1" } }, "stable paths": [