nf-core · mashehu · Apr 11, 2024 · Apr 12, 2024 · Apr 12, 2024 · Apr 14, 2024
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -15,7 +15,6 @@ jobs:
     steps:
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -39,7 +39,6 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,2 +1,7 @@
 repository_type: pipeline
+lint:
+  files_unchanged:
+    - assets/nf-core-pairgenomealign_logo_light.png
+    - docs/images/nf-core-pairgenomealign_logo_light.png
+    - docs/images/nf-core-pairgenomealign_logo_dark.png
 nf_core_version: "2.14.1"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,14 +3,6 @@
 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).
 
-## v1.0dev - [date]
+## v1.0.0 "Sweet potato" - [July 19th, 2024]
 
 Initial release of nf-core/pairgenomealign, created with the [nf-core](https://nf-co.re/) template.
-
-### `Added`
-
-### `Fixed`
-
-### `Dependencies`
-
-### `Deprecated`
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -8,11 +8,23 @@
 
 > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
 
+## Pipeline design
+
+> Charles Plessy, Michael J. Mansfield, Aleksandra Bliznina, Aki Masunaga, Charlotte West, Yongkai Tan, Andrew W. Liu, Jan Grašič, María Sara del Río Pisula, Gaspar Sánchez-Serna, Marc Fabrega-Torrus, Alfonso Ferrández-Roldán, Vittoria Roncalli, Pavla Navratilova, Eric M. Thompson, Takeshi Onuma, Hiroki Nishida, Cristian Cañestro, Nicholas M. Luscombe. Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species. Genome Res. 2024. 34: 426-440; doi: [10.1101/2023.05.09.539028](https://doi.org/10.1101/gr.278295.123). PubMed ID: [38621828](https://pubmed.ncbi.nlm.nih.gov/38621828/)
+
 ## Pipeline tools
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [LAST](https://gitlab.com/mcfrith/last/)
+
+  > Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 21(3):487-93. doi: 10.1101/gr.113985.110. PubMed PMID: 21209072 (This describes the main algorithms used by LAST.)
+
+  > Frith MC, Noé L. Improved search heuristics find 20,000 new alignments between human and mouse genomes. doi: 10.1093/nar/gku104 PubMed PMID: 24493737 (This describes sensitive DNA seeding (MAM8 and MAM4)
+
+  > Frith MC, Kawaguchi R. Split-alignment of genomes finds orthologies more accurately. Genome Biology. 2015 16:106. doi: 10.1186/s13059-015-0670-9 PubMed PMID: 25994148 (Describes the split alignment algorithm, and its application to whole genome alignment.)
+
+  > Hamada M, Ono Y, Asai K Frith MC. Training alignment parameters for arbitrary sequencers with LAST-TRAIN. Bioinformatics. 2017 33(6):926-928. doi: 10.1093/bioinformatics/btw742 PubMed PMID: 28039163 (Describes last-train.)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+  > Frith MC, Shaw J, Spouge JL. How to optimally sample a sequence for rapid analysis. doi: 10.1093/bioinformatics/btad057 PubMed PMID: 36702468 (Describes the lastdb -u RY sparsity options.)
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 

diff --git a/README.md b/README.md
@@ -19,49 +19,37 @@
 
 ## Introduction
 
-**nf-core/pairgenomealign** is a bioinformatics pipeline that ...
+**nf-core/pairgenomealign** is a bioinformatics pipeline that aligns one or more _query_ genomes to a _target_ genome, and plots pairwise representations.
 
-<!-- TODO nf-core:
-   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
-   major pipeline sections and the types of output it produces. You're giving an overview to someone new
-   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
--->
+![Tubemap workflow summary](docs/images/pairgenomealign-tubemap.png "Tubemap workflow summary")
 
-<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+The pipeline can generate four kinds of outputs, called _many-to-many_, _many-to-one_, _one-to-many_ and _one-to-one_, depending on whether sequences of one genome are allowed match the other genome multiple times or not.
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+These alignments are output in [MAF](https://genome.ucsc.edu/FAQ/FAQformat.html#format5) format, and optional line plot representations are output in PNG format.
 
 ## Usage
 
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
 
 ```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+sample,fasta
+query_1,path-to-query-genome-file-one.fasta
+query_2,path-to-query-genome-file-two.fasta
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
-
--->
+Each row represents a fasta file, this can also contain multiple rows to accomodate multiple query genomes in fasta format.
 
 Now, you can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/pairgenomealign \
    -profile <docker/singularity/.../institute> \
+   --target sequencefile.fa \
    --input samplesheet.csv \
    --outdir <OUTDIR>
 ```
@@ -80,11 +68,11 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/pairgenomealign was originally written by charles-plessy.
+`nf-core/pairgenomealign` was originally written by [charles-plessy](https://github.com/charles-plessy); the original versions are available at <https://github.com/oist/plessy_pairwiseGenomeComparison>.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+- [Mahdi Mohammed](https://github.com/U13bs1125): ported the original pipeline to _nf-core_ template 2.14.x.
 
 ## Contributions and Support
 
@@ -94,10 +82,15 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/pairgenomealign for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+If you use this pipeline, please cite:
+
+> **Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species.**
+> Charles Plessy, Michael J. Mansfield, Aleksandra Bliznina, Aki Masunaga, Charlotte West, Yongkai Tan, Andrew W. Liu, Jan Grašič, María Sara del Río Pisula, Gaspar Sánchez-Serna, Marc Fabrega-Torrus, Alfonso Ferrández-Roldán, Vittoria Roncalli, Pavla Navratilova, Eric M. Thompson, Takeshi Onuma, Hiroki Nishida, Cristian Cañestro, Nicholas M. Luscombe.
+> _Genome Res._ 2024. 34: 426-440; doi: [10.1101/2023.05.09.539028](https://doi.org/10.1101/gr.278295.123). PubMed ID: [38621828](https://pubmed.ncbi.nlm.nih.gov/38621828/)
+
+[OIST research news article](https://www.oist.jp/news-center/news/2024/4/25/oikopleura-who-species-identity-crisis-genome-community)
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+And also please cite the [LAST papers](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-papers.rst).
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
@@ -3,7 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/pairgenomealign Methods Description"
 section_href: "https://github.com/nf-core/pairgenomealign"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/tree/dev" target="_blank">nf-core/pairgenomealign</a>
+  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/releases/tag/1.0.0" target="_blank">nf-core/pairgenomealign</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/pairgenomealign/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/pairgenomealign/1.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-pairgenomealign-methods-description":
     order: -1000
@@ -13,3 +13,19 @@ report_section_order:
 export_plots: true
 
 disable_version_detection: true
+
+custom_data:
+  train:
+    file_format: "tsv"
+    section_name: "Training parameter statistics"
+    plot_type: "table"
+  last_o2o:
+    file_format: "tsv"
+    section_name: "Alignment statistics"
+    plot_type: "table"
+
+sp:
+  last_o2o:
+    fn: "*o2o_aln.tsv"
+  train:
+    fn: "*train.tsv"
diff --git a/assets/samplesheet_full.csv b/assets/samplesheet_full.csv
@@ -0,0 +1,35 @@
+sample,fasta
+Homo_sapiens_GCA_000001405.29,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.29_GRCh38.p14/GCA_000001405.29_GRCh38.p14_genomic.fna.gz
+Callithrix_jacchus_GCA_000004665.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/004/665/GCA_000004665.1_Callithrix_jacchus-3.2/GCA_000004665.1_Callithrix_jacchus-3.2_genomic.fna.gz
+Cercopithecus_mitis_GCA_028627265.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/627/265/GCA_028627265.1_Cercopithecus_mitis_HiC/GCA_028627265.1_Cercopithecus_mitis_HiC_genomic.fna.gz
+Chlorocebus_sabaeus_GCA_000409795.2,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/409/795/GCA_000409795.2_Chlorocebus_sabeus_1.1/GCA_000409795.2_Chlorocebus_sabeus_1.1_genomic.fna.gz
+Colobus_guereza_GCA_030247045.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/030/247/045/GCA_030247045.1_ASM3024704v1/GCA_030247045.1_ASM3024704v1_genomic.fna.gz
+Eulemur_mongoz_GCA_028534055.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/534/055/GCA_028534055.1_Eulemur_mongoz_HiC/GCA_028534055.1_Eulemur_mongoz_HiC_genomic.fna.gz
+Gorilla_gorilla_gorilla_GCA_000151905.3,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/151/905/GCA_000151905.3_gorGor4/GCA_000151905.3_gorGor4_genomic.fna.gz
+Hylobates_pileatus_GCA_021498465.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/021/498/465/GCA_021498465.1_ASM2149846v1/GCA_021498465.1_ASM2149846v1_genomic.fna.gz
+Lemur_catta_GCA_020740605.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/740/605/GCA_020740605.1_mLemCat1.pri/GCA_020740605.1_mLemCat1.pri_genomic.fna.gz
+Leontopithecus_rosalia_GCA_028533165.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/533/165/GCA_028533165.1_Leontopithecus_rosalia_HiC/GCA_028533165.1_Leontopithecus_rosalia_HiC_genomic.fna.gz
+Macaca_cyclopis_GCA_026956025.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/956/025/GCA_026956025.1_MCyc01/GCA_026956025.1_MCyc01_genomic.fna.gz
+Macaca_fascicularis_GCA_011100615.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/GCA_011100615.1_Macaca_fascicularis_6.0_genomic.fna.gz
+Macaca_mulatta_GCA_003339765.3,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/339/765/GCA_003339765.3_Mmul_10/GCA_003339765.3_Mmul_10_genomic.fna.gz
+Macaca_thibetana_thibetana_GCA_024542745.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/024/542/745/GCA_024542745.1_ASM2454274v1/GCA_024542745.1_ASM2454274v1_genomic.fna.gz
+Microcebus_murinus_GCA_000165445.3,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/165/445/GCA_000165445.3_Mmur_3.0/GCA_000165445.3_Mmur_3.0_genomic.fna.gz
+Miopithecus_talapoin_GCA_028551445.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/551/445/GCA_028551445.1_Miopithecus_talapoin_HiC/GCA_028551445.1_Miopithecus_talapoin_HiC_genomic.fna.gz
+Nasalis_larvatus_GCA_000772465.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/772/465/GCA_000772465.1_Charlie1.0/GCA_000772465.1_Charlie1.0_genomic.fna.gz
+Nomascus_leucogenys_GCA_000146795.3,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/146/795/GCA_000146795.3_Nleu_3.0/GCA_000146795.3_Nleu_3.0_genomic.fna.gz
+Nycticebus_bengalensis_GCA_023898255.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/023/898/255/GCA_023898255.1_ASM2389825v1/GCA_023898255.1_ASM2389825v1_genomic.fna.gz
+Nycticebus_coucang_GCA_027406575.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/027/406/575/GCA_027406575.1_mNycCou1.pri/GCA_027406575.1_mNycCou1.pri_genomic.fna.gz
+Pan_paniscus_GCA_000258655.2,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/258/655/GCA_000258655.2_panpan1.1/GCA_000258655.2_panpan1.1_genomic.fna.gz
+Pan_troglodytes_GCA_000001515.5,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/515/GCA_000001515.5_Pan_tro_3.0/GCA_000001515.5_Pan_tro_3.0_genomic.fna.gz
+Papio_anubis_GCA_000264685.2,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/264/685/GCA_000264685.2_Panu_3.0/GCA_000264685.2_Panu_3.0_genomic.fna.gz
+Papio_papio_GCA_028645565.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/645/565/GCA_028645565.1_Papio_papio_HiC/GCA_028645565.1_Papio_papio_HiC_genomic.fna.gz
+Piliocolobus_tephrosceles_GCA_002776525.5,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/776/525/GCA_002776525.5_ASM277652v5/GCA_002776525.5_ASM277652v5_genomic.fna.gz
+Pithecia_pithecia_GCA_028551515.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/551/515/GCA_028551515.1_Pithecia_pithecia_HiC/GCA_028551515.1_Pithecia_pithecia_HiC_genomic.fna.gz
+Pongo_abelii_GCA_028885655.2,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/885/655/GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri/GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri_genomic.fna.gz
+Pongo_pygmaeus_GCA_028885625.2,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/885/625/GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri/GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri_genomic.fna.gz
+Rhinopithecus_roxellana_GCA_007565055.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/007/565/055/GCA_007565055.1_ASM756505v1/GCA_007565055.1_ASM756505v1_genomic.fna.gz
+Saguinus_midas_GCA_021498475.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/021/498/475/GCA_021498475.1_ASM2149847v1/GCA_021498475.1_ASM2149847v1_genomic.fna.gz
+Saguinus_oedipus_GCA_031835075.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/031/835/075/GCA_031835075.1_ASM3183507v1/GCA_031835075.1_ASM3183507v1_genomic.fna.gz
+Symphalangus_syndactylus_GCA_028878055.3,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/878/055/GCA_028878055.3_NHGRI_mSymSyn1-v2.1_pri/GCA_028878055.3_NHGRI_mSymSyn1-v2.1_pri_genomic.fna.gz
+Theropithecus_gelada_GCA_003255815.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/255/815/GCA_003255815.1_Tgel_1.0/GCA_003255815.1_Tgel_1.0_genomic.fna.gz
+Varecia_variegata_GCA_028533085.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/028/533/085/GCA_028533085.1_Varecia_variegata_HiC/GCA_028533085.1_Varecia_variegata_HiC_genomic.fna.gz
diff --git a/assets/samplesheet_small.csv b/assets/samplesheet_small.csv
@@ -0,0 +1,3 @@
+sample,fasta
+Fusarium_asiaticum_GCA_025258505.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/025/258/505/GCA_025258505.1_ASM2525850v1/GCA_025258505.1_ASM2525850v1_genomic.fna.gz
+Fusarium_oxysporum_GCA_014857085.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/857/085/GCA_014857085.1_ASM1485708v1/GCA_014857085.1_ASM1485708v1_genomic.fna.gz
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -13,21 +13,14 @@
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
                 "meta": ["id"]
             },
-            "fastq_1": {
+            "fasta": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
-            },
-            "fastq_2": {
-                "type": "string",
-                "format": "file-path",
-                "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "pattern": "^\\S+\\.f(ast|n)?a(\\.gz)?$",
+                "errorMessage": "Fasta file for genomes must be provided, cannot contain spaces and must have extension `.fa`, `.fa.gz`, `.fna`, `.fna.gz`, `.fasta` or `.fasta.gz`"
             }
         },
-        "required": ["sample", "fastq_1"]
+        "required": ["sample", "fasta"]
     }
 }
diff --git a/conf/base.config b/conf/base.config
@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
@@ -24,7 +23,6 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { check_max( 1                  , 'cpus'    ) }