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Recent Releases of blobtoolkit

blobtoolkit - v0.8.0 – Sprigatito

Enhancements & fixes

  • Runtime of the blast commands is now capped at 12 hours (#166)
  • Upgraded Busco and added an option to control the gene predictor used (#160, #174, #181)
  • nf-core template upgrade (to version 3.2.1) (#164, #176)
  • Documentation fixes (broken links) (#175)
  • Ability to run without any read data (#177)

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. 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 | | ----------- | ----------- | ----------- | | blobtoolkit | 4.4.4 | 4.4.6 | | busco | 5.7.1 | 5.8.3 |

Parameters

| Old parameter | New parameter | | ------------- | ---------------------- | | | --buscogenepredictor |

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.

- Nextflow
Published by muffato 9 months ago

blobtoolkit - v0.7.1 – Psyduck (patch 1)

Enhancements & fixes

  • Upgraded the blobtools version which contains a bugfix

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. 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 | | ----------- | ----------- | ----------- | | blobtoolkit | 4.4.4 | 4.4.5 |

- Nextflow
Published by muffato 11 months ago

blobtoolkit - v0.7.0 – Psyduck

Enhancements & fixes

  • Fetch information about the chromosomes of the assemblies. Used to power "grid plots".
  • Fill in accurate read information in the blobDir. Users are now reqiured to indicate in the samplesheet whether the reads are paired or single.
  • Updated the Blastn settings to allow 7 days runtime at most, since that covers 99.7% of the jobs.
  • Allow database inputs to be optionally compressed (.tar.gz)
  • Allow BUSCO run outputs to be optionally pre-computed and provided with --precomputed_busco

The pipeline is now considered to be a complete and suitable replacement for the Snakemake version with the caveats that:

  • Resource requirements (CPU and memory) of the processes aren't optimal.
  • The Blastn step can take up to a week to run.

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. 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 | | ----------- | ----------------- | --------------- | | blast | 2.14.1 and 2.15.0 | only 2.15.0 | | blobtoolkit | 4.3.9 | 4.4.4 | | busco | 5.5.0 | 5.7.1 | | multiqc | 1.20 and 1.21 | 1.20 and 1.25.1 | | samtools | 1.18 and 1.19.2 | 1.20 and 1.21 |

Parameters

| Old parameter | New parameter | | ------------- | ------------------- | | | --precomputed_busco |

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.

- Nextflow
Published by muffato 11 months ago

blobtoolkit - v0.6.0 – Bellsprout

[0.6.0] – Bellsprout – [2024-09-13]

The pipeline has now been validated for draft (unpublished) assemblies.

  • The pipeline now queries the NCBI database instead of GoaT to establish the taxonomic classification of the species and the relevant Busco lineages. In case the taxonid is not found, the pipeline falls back to GoaT, which is aware of upcoming taxonids in ENA.
  • New --busco_lineages parameter to choose specific Busco lineages instead of automatically selecting based on the taxonomy.
  • All parameters are now passed the regular Nextflow way. There is no support for the original Yaml configuration files of the Snakemake version.
  • New option --skip_taxon_filtering to skip the taxon filtering in blast searches. Mostly relevant for draft assemblies.
  • Introduced the --use_work_dir_as_temp parameter to avoid leaving files in /tmp.

Parameters

| Old parameter | New parameter | | ------------- | ---------------------- | | --yaml | | | | --buscolineages | | | --skiptaxonfiltering | | | --useworkdiras_temp |

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. 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 | | ---------- | ----------- | ----------- | | goat | 0.2.5 | |

- Nextflow
Published by muffato over 1 year ago

blobtoolkit - v0.5.1 – Snorlax (patch 1)

[0.5.1] – Snorlax (patch 1) – [2024-08-22]

Enhancements & fixes

  • Bugfix: skip BLASTN if there are no chunks to align

- Nextflow
Published by muffato over 1 year ago

blobtoolkit - v0.5.0 – Snorlax

[0.5.0] – Snorlax – [2024-07-31]

General tidy up of the configuration and the pipeline

Enhancements & fixes

  • Increased the resources for blastn
  • Removed some options that were not used or not needed
  • All relevant outputs are now copied to the output directory
  • Fixed some blast parameters to match the behaviour of the Snakemake pipeline
  • Fixed parsing of samplesheets from fetchngs to capture correct data type

Parameters

| Old parameter | New parameter | | --------------- | ------------- | | --taxafile | | | --blastpoutext | | | --blastpcols | | | --blastxoutext | | | --blastx_cols | |

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.

- Nextflow
Published by muffato over 1 year ago

blobtoolkit - v0.4.0 – Buneary

[0.4.0] – Buneary – [2024-04-17]

The pipeline has now been validated on dozens of genomes, up to 11 Gbp.

Enhancements & fixes

  • Upgraded the version of blobtools, which enables a better reporting of wrong accession numbers and a better handling of oddities in input files.
  • Files in the output blobdir are now compressed.
  • All modules handling blobdirs can now be cached.
  • Large genomes supported, up to at least 11 Gbp.
  • Allow all variations of FASTA and FASTQ extensions for input.
  • More fields included in the trace files.
  • All nf-core modules updated

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. 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 | | ----------- | ------------- | ------------- | | blobtoolkit | 4.3.3 | 4.3.9 | | blast | 2.14.0 | 2.15.0 | | multiqc | 1.17 and 1.18 | 1.20 and 1.21 | | samtools | 1.18 | 1.19.2 | | seqtk | 1.3 | 1.4 |

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.

- Nextflow
Published by muffato almost 2 years ago

blobtoolkit - v0.3.0 – Poliwag

[0.3.0] – Poliwag – [2024-02-09]

The pipeline has now been validated on five genomes, all under 100 Mbp: a sponge, a platyhelminth, and three fungi.

Enhancements & fixes

  • Fixed the conditional runs of blastn
  • Fixed the generation of the no-hit list
  • Fixed the conversion of the unaligned input files to Fasta
  • Fixed the documentation about preparing the NT database
  • Fixed the detection of the NT database in the nf-core module
  • The pipeline now supports samplesheets generated by the nf-core/fetchngs pipeline by passing the --fetchngs_samplesheet true option.
  • FastQ files can bypass the conversion to Fasta
  • Fixed missing BUSCO results from the blobdir (only 1 BUSCO was loaded)
  • Fixed the default category used to colour the blob plots
  • Fixed the output directory of the images
  • Added an option to select the format of the images (PNG or SVG)

Parameters

| Old parameter | New parameter | | ------------- | ---------------------- | | | --fetchngssamplesheet | | | --imageformat |

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.

- Nextflow
Published by muffato about 2 years ago

blobtoolkit - v0.2.0 – Pikachu

[0.2.0] – Pikachu – [2023-12-22]

Enhancements & fixes

  • Template updated to nf-core/tools 2.11.1
  • Includes all subworkflows in the Snakemake version
  • Added blastx and blastn subworkflows
  • Replaced mosdepth with blobtk depth
  • Updated config creation script

Parameters

| Old parameter | New parameter | | ------------- | --------------- | | | --mask | | | --align | | --uniprot | --blastp | | | --blastx | | | --blastn | | | --blastxoutext | | | --blastxcols |

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. 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 | | ------------ | ----------- | ----------- | | blobtoolkit | 4.1.4 | 4.3.2 | | busco | 5.4.3 | 5.5.0 | | goat | 0.2.0 | 0.2.5 | | mosdepth | 0.3.3 | | | nextflow | 22.10.6 | 23.10.0 | | python | 3.10.6 | 3.12.0 | | samtools | 1.15.1 | 1.18 | | tar | 1.30 | | | yaml | 6.0 | 6.0.1 | | blobtk | 0.3.3 | 0.5.1 | | diamond | 2.0.15 | 2.1.8 | | minimap2 | | 2.24-r1122 | | blast | | 2.14.1 | | windowmasker | | 2.14.0 |

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.

- Nextflow
Published by priyanka-surana about 2 years ago

blobtoolkit - sanger-tol/blobtoolkit v0.1.0 – Vaporeon

[0.1.0] – Vaporeon – [2023-05-18]

Enhancements & fixes

Initial release of sanger-tol/blobtoolkit :tada:

This release marks the point where the pipeline was moved from Snakemake at blobtoolkit/blobtoolkit over to Nextflow DSL2 at sanger-tol/blobtoolkit. There are two subworkflows in the Snakemake version that are still being implemented in Nextflow – diamond_blastx and blastn.

Parameters

| Old parameter | New parameter | | ------------- | --------------- | | | --input | | | --fasta | | | --accession | | | --taxon | | | --taxafile | | | --yaml | | | --blastpoutext | | | --blastp_cols | | | --taxdump | | | --busco | | | --uniprot |

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. 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 | | ------------- | ----------- | ----------- | | blobtoolkit | | 4.1.4 | | busco | | 5.4.3 | | fasta_windows | | 0.2.4 | | goat | | 0.2.0 | | gunzip | | 1.10 | | mosdepth | | 0.3.3 | | nextflow | | 22.10.6 | | python | | 3.10.6 | | samtools | | 1.15.1 | | tar | | 1.30 | | yaml | | 6.0 |

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.

- Nextflow
Published by priyanka-surana almost 3 years ago