sanger-tol · muffato · Oct 3, 2025 · Jul 15, 2025 · Jul 16, 2025 · Jul 16, 2025
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -43,4 +43,4 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 0.8.0
+  version: 0.9.0
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,27 @@
 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).
 
+## [[0.9.0](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.9.0)] – Scyther – [2025-10-03]
+
+### Enhancements & fixes
+
+- Upgrade Busco (#190)
+- The pipeline now stops on Busco failures (#194)
+- Update resource requirements for BLASTN modules (#191) and BLOBTOOLKIT_WINDOWSTATS
+- Fixed the `test_full` profile (Sanger only)
+- Addition of `--tmpdir` to Diamond blast modules (#200)
+- `--use_work_dir_as_temp` is no longer a hidden param.
+- Fixed some documentation (#193 and #197)
+- Made GENERATE_CONFIG more resilient to network errors (#197)
+
+### Software dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only `Docker` or `Singularity` containers are supported, `conda` is not supported.
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| busco      | 5.8.3       | 6.0.0       |
+
 ## [[0.8.0](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.8.0)] – Sprigatito – [2025-05-19]
 
 ### Enhancements & fixes

diff --git a/CITATION.cff b/CITATION.cff
@@ -27,6 +27,12 @@ authors:
     given-names: Matthieu
     orcid: https://orcid.org/0000-0002-7860-3560
     website: https://github.com/muffato
+  - affiliation: Wellcome Sanger Institute
+    email: dp24@sanger.ac.uk
+    family-names: Pointon
+    given-names: Damon-Lee Bernard
+    orcid: https://orcid.org/0000-0003-2949-6719
+    website: https://github.com/DLBPointon
   - affiliation: Wellcome Sanger Institute
     email: 729395+gq1@users.noreply.github.com
     family-names: Qi
@@ -57,13 +63,13 @@ authors:
     orcid: https://orcid.org/0000-0003-1658-1762
     website: https://github.com/BethYates
 cff-version: 1.2.0
-date-released: "2025-04-25"
+date-released: "2025-10-03"
 doi: 10.5281/zenodo.7949058
 license: MIT
 message: If you use this software, please cite it using the metadata from this file
   and all references from CITATIONS.md .
 repository-code: https://github.com/sanger-tol/blobtoolkit
-title: sanger-tol/blobtoolkit v0.8.0 -
+title: sanger-tol/blobtoolkit v0.9.0 - Scyther
 type: software
 url: https://pipelines.tol.sanger.ac.uk/blobtoolkit
-version: 0.8.0
+version: 0.9.0
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -1,71 +1,77 @@
 # sanger-tol/blobtoolkit: Citations
 
-> Butt, Zaynab, et al. "sanger-tol/blobtoolkit" Zenodo, 2023, https://zenodo.org/doi/10.5281/zenodo.7949058.
+> Butt, Zaynab, et al. "sanger-tol/blobtoolkit" Zenodo, 2023, <https://zenodo.org/doi/10.5281/zenodo.7949058>
 
 ## [nf-core](https://nf-co.re)
 
-> Ewels, Philip A., et al. “The Nf-Core Framework for Community-Curated Bioinformatics Pipelines.” Nature Biotechnology, vol. 38, no. 3, Feb. 2020, pp. 276–78, https://doi.org/10.1038/s41587-020-0439-x.
+> Ewels, Philip A., et al. “The Nf-Core Framework for Community-Curated Bioinformatics Pipelines.” Nature Biotechnology, vol. 38, no. 3, Feb. 2020, pp. 276–78, <https://doi.org/10.1038/s41587-020-0439-x>
 
 ## [Nextflow](https://www.nextflow.io)
 
-> Di Tommaso, Paolo, et al. “Nextflow Enables Reproducible Computational Workflows.” Nature Biotechnology, vol. 35, no. 4, Apr. 2017, pp. 316–19, https://doi.org/10.1038/nbt.3820.
+> Di Tommaso, Paolo, et al. “Nextflow Enables Reproducible Computational Workflows.” Nature Biotechnology, vol. 35, no. 4, Apr. 2017, pp. 316–19, <https://doi.org/10.1038/nbt.3820>
 
 ## Pipeline tools
 
 - [BLAST+](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html)
 
-  > Camacho, Chritiam, et al. “BLAST+: architecture and applications.” BMC Bioinformatics, vol. 10, no. 412, Dec. 2009, https://doi.org/10.1186/1471-2105-10-421
+  > Camacho, Chritiam, et al. “BLAST+: architecture and applications.” BMC Bioinformatics, vol. 10, no. 412, Dec. 2009, <https://doi.org/10.1186/1471-2105-10-421>
+
+- [BlobTk](https://github.com/genomehubs/blobtk)
 
 - [BlobToolKit](https://github.com/blobtoolkit/blobtoolkit)
 
-  > Challis, Richard, et al. “BlobToolKit – Interactive Quality Assessment of Genome Assemblies.” G3 Genes|Genomes|Genetics, vol. 10, no. 4, Apr. 2020, pp. 1361–74, https://doi.org/10.1534/g3.119.400908.
+  > Challis, Richard, et al. “BlobToolKit – Interactive Quality Assessment of Genome Assemblies.” G3 Genes|Genomes|Genetics, vol. 10, no. 4, Apr. 2020, pp. 1361–74, <https://doi.org/10.1534/g3.119.400908>
 
 - [BUSCO](https://gitlab.com/ezlab/busco)
 
-  > Manni, Mosè, et al. “BUSCO: Assessing Genomic Data Quality and Beyond.” Current Protocols, vol. 1, no. 12, Dec. 2021, https://doi.org/10.1002/cpz1.323.
+  > Manni, Mosè, et al. “BUSCO: Assessing Genomic Data Quality and Beyond.” Current Protocols, vol. 1, no. 12, Dec. 2021, <https://doi.org/10.1002/cpz1.323>
 
 - [Diamond](https://github.com/bbuchfink/diamond)
 
-  > Buchfink, Benjamin, et al. “Sensitive Protein Alignments at Tree-of-Life Scale Using DIAMOND.” Nature Methods, vol. 18, no. 4, Apr. 2021, pp. 366–68, https://doi.org/10.1038/s41592-021-01101-x.
+  > Buchfink, Benjamin, et al. “Sensitive Protein Alignments at Tree-of-Life Scale Using DIAMOND.” Nature Methods, vol. 18, no. 4, Apr. 2021, pp. 366–68, <https://doi.org/10.1038/s41592-021-01101-x>
 
 - [Fasta_windows](https://github.com/tolkit/fasta_windows)
 
-  > Brown, Max, et al. "Fasta_windows v0.2.3". GitHub, 2021. https://github.com/tolkit/fasta_windows
+  > Brown, Max, et al. "Fasta_windows v0.2.3". GitHub, 2021. <https://github.com/tolkit/fasta_windows>
 
 - [Minimap2](https://github.com/lh3/minimap2)
 
-  > Li, Heng. "Minimap2: pairwise alignment for nucleotide sequences." Bioinformatics, vol. 34, no. 18, Sep. 2018, pp. 3094-100, https://doi.org/10.1093/bioinformatics/bty191.
+  > Li, Heng. "Minimap2: pairwise alignment for nucleotide sequences." Bioinformatics, vol. 34, no. 18, Sep. 2018, pp. 3094-100, <https://doi.org/10.1093/bioinformatics/bty191>
 
 - [MultiQC](https://multiqc.info)
 
-  > Ewels, Philip, et al. “MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report.” Bioinformatics, vol. 32, no. 19, 2016, pp. 3047–3048., https://doi.org/10.1093/bioinformatics/btw354.
+  > Ewels, Philip, et al. “MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report.” Bioinformatics, vol. 32, no. 19, 2016, pp. 3047–3048., <https://doi.org/10.1093/bioinformatics/btw354>
 
 - [Samtools](https://www.htslib.org)
 
-  > Danecek, Petr, et al. “Twelve Years of SAMtools and BCFtools.” GigaScience, vol. 10, no. 2, Jan. 2021, https://doi.org/10.1093/gigascience/giab008.
+  > Danecek, Petr, et al. “Twelve Years of SAMtools and BCFtools.” GigaScience, vol. 10, no. 2, Jan. 2021, <https://doi.org/10.1093/gigascience/giab008>
 
 - [SeqTK](https://github.com/lh3/seqtk)
 
-  > Li, Heng. "SeqTK v1.4" GitHub, 2023, https://github.com/lh3/seqtk
+  > Li, Heng. "SeqTK v1.4" GitHub, 2023, <https://github.com/lh3/seqtk>
+
+- [WindowMasker](https://pubmed.ncbi.nlm.nih.gov/16287941/)
+
+  > Morgulis, A., et al. 2006. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 22(2). pp.134–141. doi: 10.1093/bioinformatics/bti774.
 
 ## Software packaging/containerisation tools
 
 - [Conda](https://conda.org/)
 
-  > conda contributors. conda: A system-level, binary package and environment manager running on all major operating systems and platforms. Computer software. https://github.com/conda/conda
+  > conda contributors. conda: A system-level, binary package and environment manager running on all major operating systems and platforms. Computer software. <https://github.com/conda/conda>
 
 - [Bioconda](https://bioconda.github.io)
 
-  > Grüning, Björn, et al. “Bioconda: sustainable and comprehensive software distribution for the life sciences.", Nature Methods, vol. 15, Jul. 2018, pp. 475-6, https://doi.org/10.1038/s41592-018-0046-7.
+  > Grüning, Björn, et al. “Bioconda: sustainable and comprehensive software distribution for the life sciences.", Nature Methods, vol. 15, Jul. 2018, pp. 475-6, <https://doi.org/10.1038/s41592-018-0046-7>
 
 - [BioContainers](https://biocontainers.pro)
 
-  > da Veiga, Felipe, et al. “BioContainers: an open-source and community-driven framework for software standardization.", Bioinformatics, vol. 33, no. 16, Aug. 2017, pp. 2580-2, https://doi.org/10.1093/bioinformatics/btx192.
+  > da Veiga, Felipe, et al. “BioContainers: an open-source and community-driven framework for software standardization.", Bioinformatics, vol. 33, no. 16, Aug. 2017, pp. 2580-2, <https://doi.org/10.1093/bioinformatics/btx192>
 
 - [Docker](https://www.docker.com)
 
   > Merkel, Dirk, et al. “Docker: Lightweight Linux Containers for Consistent Development and Deployment.", Association for Computing Machinery, vol. 2014, no. 239, Mar. 2014.
 
 - [Singularity](https://docs.sylabs.io/guides/latest/user-guide/)
 
-  > Kurtzer, Gregory M., et al. “Singularity: Scientific containers for mobility of compute.", PLOS ONE, vol. 12, no. 5, May 2017, pp. e0177459, https://doi.org/10.1371/journal.pone.0177459.
+  > Kurtzer, Gregory M., et al. “Singularity: Scientific containers for mobility of compute.", PLOS ONE, vol. 12, no. 5, May 2017, pp. e0177459, <https://doi.org/10.1371/journal.pone.0177459>
diff --git a/README.md b/README.md
@@ -1,7 +1,8 @@
 # ![sanger-tol/blobtoolkit](docs/images/sanger-tol-blobtoolkit_logo.png)
 
 [![GitHub Actions CI Status](https://github.com/sanger-tol/blobtoolkit/actions/workflows/ci.yml/badge.svg)](https://github.com/sanger-tol/blobtoolkit/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/sanger-tol/blobtoolkit/actions/workflows/linting.yml/badge.svg)](https://github.com/sanger-tol/blobtoolkit/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7949058-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7949058)
+[![GitHub Actions Linting Status](https://github.com/sanger-tol/blobtoolkit/actions/workflows/linting.yml/badge.svg)](https://github.com/sanger-tol/blobtoolkit/actions/workflows/linting.yml)
+[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7949058-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7949058)
 
 <!--[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)-->
 
@@ -23,10 +24,10 @@ It takes a samplesheet of BAM/CRAM/FASTQ/FASTA files as input, calculates genome
 5. Extract BUSCO genes ([`blobtoolkit/extractbuscos`](https://github.com/blobtoolkit/blobtoolkit))
 6. Run Diamond BLASTp against extracted BUSCO genes ([`diamond/blastp`](https://github.com/bbuchfink/diamond))
 7. Run BLASTx against sequences with no hit ([`diamond/blastx`](https://github.com/bbuchfink/diamond))
-8. Run BLASTn against sequences still with not hit ([`blast/blastn`](https://www.ncbi.nlm.nih.gov/books/NBK131777/))
+8. Run BLASTn against sequences still with no hit ([`blast/blastn`](https://www.ncbi.nlm.nih.gov/books/NBK131777/))
 9. Count BUSCO genes ([`blobtoolkit/countbuscos`](https://github.com/blobtoolkit/blobtoolkit))
 10. Generate combined sequence stats across various window sizes ([`blobtoolkit/windowstats`](https://github.com/blobtoolkit/blobtoolkit))
-11. Imports analysis results into a BlobDir dataset ([`blobtoolkit/blobdir`](https://github.com/blobtoolkit/blobtoolkit))
+11. Import analysis results into a BlobDir dataset ([`blobtoolkit/blobdir`](https://github.com/blobtoolkit/blobtoolkit))
 12. Create static plot images ([`blobtk/images`](https://github.com/blobtoolkit/blobtk))
 
 ## Usage
@@ -40,13 +41,14 @@ First, prepare a samplesheet with your input data that looks as follows:
 
 ```csv
 sample,datatype,datafile,library_layout
-mMelMel3,hic,GCA_922984935.2.hic.mMelMel3.cram,PAIRED
+mMelMel3_hic,hic,GCA_922984935.2.hic.mMelMel3.cram,PAIRED
 mMelMel1,illumina,GCA_922984935.2.illumina.mMelMel1.cram,PAIRED
-mMelMel3,ont,GCA_922984935.2.ont.mMelMel3.cram,SINGLE
+mMelMel3_ont,ont,GCA_922984935.2.ont.mMelMel3.cram,SINGLE
 ```
 
-Each row represents an aligned file.
-Rows with the same sample identifier are considered technical replicates.
+Each row represents a read set (aligned or not).
+The first column (sample name) must be unique.
+If you have multiple read sets from the same actual sample, make sure you edit the sample names to make them unique.
 The datatype refers to the sequencing technology used to generate the underlying raw data and follows a controlled vocabulary (`ont`, `hic`, `pacbio`, `pacbio_clr`, `illumina`).
 The library layout indicates whether the reads are paired or single.
 The aligned read files can be generated using the [sanger-tol/readmapping](https://github.com/sanger-tol/readmapping) pipeline.
@@ -78,9 +80,19 @@ For more details about the output files and reports, please refer to the [output
 
 ## Credits
 
-sanger-tol/blobtoolkit was written in Nextflow by [Alexander Ramos Diaz](https://github.com/alxndrdiaz), [Zaynab Butt](https://github.com/zb32), [Matthieu Muffato](https://github.com/muffato), and [Priyanka Surana](https://github.com/priyanka-surana). The orignal design and coding for [BlobToolKit software and Snakemake pipeline](https://github.com/blobtoolkit/blobtoolkit) was done by [Richard Challis](https://github.com/rjchallis) and [Sujai Kumar](https://github.com/sujaikumar).
+sanger-tol/blobtoolkit was written in Nextflow by:
 
-We thank the following people for their assistance in the development of this pipeline:
+- [Alexander Ramos Diaz](https://github.com/alxndrdiaz)
+- [Zaynab Butt](https://github.com/zb32)
+- [Priyanka Surana](https://github.com/priyanka-surana)
+- [Matthieu Muffato](https://github.com/muffato)
+- [Tyler Chafin](https://github.com/tkchafin)
+- [Yumi Sims](https://github.com/yumisims)
+- [Damon-Lee Bernard Pointon](https://github.com/DLBPointon)
+
+The original design and coding for [BlobToolKit software and Snakemake pipeline](https://github.com/blobtoolkit/blobtoolkit) was done by [Richard Challis](https://github.com/rjchallis) and [Sujai Kumar](https://github.com/sujaikumar).
+
+We thank the following people for their extensive assistance in the development of this pipeline:
 
 - [Guoying Qi](https://github.com/gq1)
 - [Bethan Yates](https://github.com/BethYates)
@@ -91,7 +103,7 @@ If you would like to contribute to this pipeline, please see the [contributing g
 
 ## Citations
 
-If you use sanger-tol/blobtoolkit for your analysis, please cite it using the following doi: [10.5281/zenodo.7949058](https://doi.org/10.5281/zenodo.7949058)
+If you use sanger-tol/blobtoolkit for your analysis, please cite it using the following DOI: [10.5281/zenodo.7949058](https://doi.org/10.5281/zenodo.7949058)
 
 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/schema_input.json b/assets/schema_input.json
@@ -9,7 +9,7 @@
         "properties": {
             "sample": {
                 "type": "string",
-                "description": "Sample Name",
+                "description": "Sample identifier",
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided, be unique, and cannot contain spaces",
                 "meta": ["id"]
@@ -18,7 +18,7 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "enum": ["hic", "illumina", "ont", "pacbio", "pacbio_clr"],
-                "errorMessage": "Data type, and must be one of: 'hic' or 'illumina' or 'ont' or 'pacbio'",
+                "errorMessage": "Data type must be one of: 'hic' or 'illumina' or 'ont' or 'pacbio'",
                 "meta": ["datatype"]
             },
             "datafile": {

diff --git a/assets/test/samplesheet.csv b/assets/test/samplesheet.csv
@@ -1,5 +1,5 @@
 sample,datatype,datafile,library_layout
-mMelMel3_hic,hic,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/analysis/mMelMel3.2_paternal_haplotype/read_mapping/hic/GCA_922984935.2.subset.unmasked.hic.mMelMel3.cram,PAIRED
-mMelMel1,illumina,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/analysis/mMelMel3.2_paternal_haplotype/read_mapping/illumina/GCA_922984935.2.subset.unmasked.illumina.mMelMel1.cram,PAIRED
-mMelMel2,illumina,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/analysis/mMelMel3.2_paternal_haplotype/read_mapping/illumina/GCA_922984935.2.subset.unmasked.illumina.mMelMel2.cram,PAIRED
-mMelMel3_ont,ont,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/analysis/mMelMel3.2_paternal_haplotype/read_mapping/ont/GCA_922984935.2.subset.unmasked.ont.mMelMel3.cram,SINGLE
+mMelMel3_hic,hic,/nfs/treeoflife-01/resources/nextflow/test-data/Meles_meles/analysis/mMelMel3.2_paternal_haplotype/read_mapping/hic/GCA_922984935.2.subset.unmasked.hic.mMelMel3.cram,PAIRED
+mMelMel1,illumina,/nfs/treeoflife-01/resources/nextflow/test-data/Meles_meles/analysis/mMelMel3.2_paternal_haplotype/read_mapping/illumina/GCA_922984935.2.subset.unmasked.illumina.mMelMel1.cram,PAIRED
+mMelMel2,illumina,/nfs/treeoflife-01/resources/nextflow/test-data/Meles_meles/analysis/mMelMel3.2_paternal_haplotype/read_mapping/illumina/GCA_922984935.2.subset.unmasked.illumina.mMelMel2.cram,PAIRED
+mMelMel3_ont,ont,/nfs/treeoflife-01/resources/nextflow/test-data/Meles_meles/analysis/mMelMel3.2_paternal_haplotype/read_mapping/ont/GCA_922984935.2.subset.unmasked.ont.mMelMel3.cram,SINGLE
diff --git a/assets/test/samplesheet_raw.csv b/assets/test/samplesheet_raw.csv
@@ -1,4 +1,4 @@
 sample,datatype,datafile,library_layout
-mMelMel1,illumina,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel1/illumina/31231_3#1_subset.cram,PAIRED
-mMelMel2,illumina,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel2/illumina/31231_4#1_subset.cram,PAIRED
-mMelMel3,hic,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1_subset.cram,PAIRED
+mMelMel1,illumina,/nfs/treeoflife-01/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel1/illumina/31231_3#1_subset.cram,PAIRED
+mMelMel2,illumina,/nfs/treeoflife-01/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel2/illumina/31231_4#1_subset.cram,PAIRED
+mMelMel3,hic,/nfs/treeoflife-01/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1_subset.cram,PAIRED
diff --git a/assets/test_full/full_samplesheet.csv b/assets/test_full/full_samplesheet.csv
@@ -1,3 +1,3 @@
 sample,datatype,datafile,library_layout
-gfLaeSulp1_hic,hic,/lustre/scratch123/tol/resources/nextflow/test-data/Laetiporus_sulphureus/analysis/gfLaeSulp1.1/read_mapping/hic/GCA_927399515.1.unmasked.hic.gfLaeSulp1.cram,PAIRED
-gfLaeSulp1_pacbio,pacbio,/lustre/scratch123/tol/resources/nextflow/test-data/Laetiporus_sulphureus/analysis/gfLaeSulp1.1/read_mapping/pacbio/GCA_927399515.1.unmasked.pacbio.gfLaeSulp1.cram,SINGLE
+gfLaeSulp1_hic,hic,/nfs/treeoflife-01/resources/nextflow/test-data/Laetiporus_sulphureus/analysis/gfLaeSulp1.1/read_mapping/hic/GCA_927399515.1.unmasked.hic.gfLaeSulp1.cram,PAIRED
+gfLaeSulp1_pacbio,pacbio,/nfs/treeoflife-01/resources/nextflow/test-data/Laetiporus_sulphureus/analysis/gfLaeSulp1.1/read_mapping/pacbio/GCA_927399515.1.unmasked.pacbio.gfLaeSulp1.cram,SINGLE