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Recent Releases of ascc

ascc - 0.4.0 - Red Mouse

[0.4.0] - Red Mouse [ 06/08/2024]

THIS IS STILL AN IN-DEVELOPMENT PROJECT SO THERE MAY BE BUGS.

Release 6 of sanger-tol/ascc, focusing on template upgrade and stability for sanger production.

Added

  • Return free-disk-space to nf-test CI runners (suggestion by @prototaxites)
  • Updated test files to post-datacentre crash (Only affects internal sanger users).
  • Test and Production (this is sanger specific, please change if you want to use the same style) configs have been updated.
  • Update to Organellar Blast subworkflow to include organellar name in output.
  • Updated some scripts for logging and linting.
  • The AUTOFILTERANDCHECK_ASSEMBLY module has been added to the ORGANELLAR subworkflow, done to ensure that sanger-tol/ascc matches previously reported statistics.
  • FCSGX Module now includes a timed backoff for when it fails, this is aimed at stopping random crashes.
  • Re-organised some of the files in the assets folder and updated configs to reflect.
  • Added a btk_pipeline.config file in assets/btk_config_files to modify btk process resource requirements. Currently contains an alternate requirement for BLASTN_TAXON.
  • Added most of the output files to the emit of the major subworkflow (GENOMIC and ORGANELLAR) this is setup for future version nf-tools which will mandate output files are treated like this.
  • Added --fcs_override and --fcs_override_samplesheet to allow the pipeline to accept externally run FCS-GX results. These results must be filteres and parsed as inside the pipeline. A wrapper script is provided as bin/ascc_fcsgx_wrapper.py.
  • Support for HAP1 and HAP2 assemblies in the samplesheet, this effects naming of output files.
  • Pipeline can now correctly handle a null value as a barcode value, removing the need for a dummy value in cases of data such as ONT which does not use barcodes.
  • Pipeline now creates a unique list of barcodes internally, stops issues where end-user scripts collect a running list of barcodes from read files.

Fixed

  • Bug where in some cases the btk_run variable would not be set prior to it's use in a conditional, causing the pipeline to crash.
  • Bug where btk input parameters would not be correctly set leading to incorrect runs of btk, where the wrong sample (no contamination) is used and the right sample is passed over.
  • Corrected an error with output of FCSGX where it was only looking for BAM files, which are not produced by FCSGX!
  • RUN_COVERAGE was using a legacy Variable name
  • Bug where fcsgx was not generating output matching cobiontcheck (predecessor to ASCC), found to be caused by an incorrect threshold value.
  • AUTOFILTER scripts were adapted to make the trigger values accessible to the end-user.
  • Other fixes introduced a race condition for sanger-tol/btk. This is now fixed and v2 of sanger-tol/ascc will wholey remove them.
  • Removed cpu and memory resource multipliers, it's not needed. If it crashes, it'll be for something else.

Bugs

  • Currently, Blobtoolkit will not run if there is no autofilter output channel.
  • tiara, fcsgx, autofilter must always be activated.

Full Changelog: https://github.com/sanger-tol/ascc/compare/0.3.0...0.4.0

- Python
Published by DLBPointon 11 months ago

ascc - 0.3.0 - Red Lamp

v0.3.0 - Red Lamp [02/05/2025]

Release 4 of sanger-toll/ascc, correcting bugs found in production testing and correcting the strucutre of the pipeline.

Enhancements & Fixes

  • Re-added the ascc.nf.
    • This corrects an issue with version generation.
  • Remove unnecessary modules which have been replaced by NF-core modules #104 .
  • Corrected incorrect file output
    • publishDir does not take a list of file extensions, only positive globs.
    • This has meant some modules have more patterns to match than previously.
    • Update modules which were outputting versions to the output dir unnecessarily.
  • Corrected issue with channel generation being tempermental in some cases.
  • Added per-process enums rather than the use of a csv list to control process execution #107.
    • Significantly easier to maintain conditionals for process execution.
    • Each unique process now has a flag such as run_{process} which accepts a value of genomic,organellar,both,off.
    • For some processes the options are genomic,both,off as they arte not useful for organellar assemblies.
    • Implemented due to feedback from users.
    • This method is now significantly easier to control and understand.
    • Due to this update we are re-introducing the genomic_only flag.
  • Update to CI and test files.
    • Includes the temporary deletion of the download_pipelines.yaml #118
    • This will require addition of databases and data to be downloaded and set up for that runner.
  • Added a production profile - intended to simplify production needs in Sanger ToL #106.
    • Updates configs for test and tol_assembly.
  • Update modules which were requesting 100.h.
  • Template has been updated to 3.2.1.
  • Updated Documentation.
  • Updated modules.config to output more files.
  • Update blobtoolkit to be using the dev branch - essential update before btk releases. #114
  • Updated FCSGX/RUNGX to version 0.5.5 #52
  • Updated the conditional logic for Blobtoolkit #123
  • Updates description to some fields - @prototaxites #121
  • Added @prototaxites as a contributor.

New Contributors

  • @prototaxites made their first contribution in https://github.com/sanger-tol/ascc/pull/113

Full Changelog: https://github.com/sanger-tol/ascc/compare/0.2.0...0.3.0

- Python
Published by DLBPointon about 1 year ago

ascc - 0.2.0 - Red Speaker

What's Changed

  • Added kmer counts dim reduction BTK figures. Edited the script of creating a BTK dataset by @eeaunin in https://github.com/sanger-tol/ascc/pull/98
  • Removing the requirement of having accession2taxid files when parsing nt BLAST results by @eeaunin in https://github.com/sanger-tol/ascc/pull/100
  • Template update 3.2 by @DLBPointon in https://github.com/sanger-tol/ascc/pull/102
    • Template Update was significant and required a non-trivial amount of time to implement.
    • Update TaxDump scripts to support new format from NCBI (11 vs 12 columns)
    • Take specified read files rather than a folder of files.
    • Update makeblastdb module
    • The structure of the project has been updated
    • Corrected conditional of ASCC
    • genomiconly removed in favour of `--organellarexclude ALL` which is a pre-existing arg for specifying work for a run.
    • Updated Blobtoolkit version and all associated scripts.
  • 0.2.0 - Release by @DLBPointon in https://github.com/sanger-tol/ascc/pull/103

Full Changelog: https://github.com/sanger-tol/ascc/compare/0.1.0...0.2.0

- Python
Published by DLBPointon about 1 year ago

ascc - v0.1.0 - Red Book

The first release of ASCC! This is still development so please create issue reports if you have issues!

What's Changed

  • Tiara by @DLBPointon in https://github.com/sanger-tol/ascc/pull/18
  • Merge pull request #18 from sanger-tol/tiara by @DLBPointon in https://github.com/sanger-tol/ascc/pull/19
  • Merge pull request #19 from sanger-tol/dev by @DLBPointon in https://github.com/sanger-tol/ascc/pull/20
  • Merge pull request #19 from sanger-tol/dev by @DLBPointon in https://github.com/sanger-tol/ascc/pull/21
  • Kraken by @DLBPointon in https://github.com/sanger-tol/ascc/pull/22
  • Dp24 modules by @DLBPointon in https://github.com/sanger-tol/ascc/pull/25
  • add fcsadaptor stuff by @yumisims in https://github.com/sanger-tol/ascc/pull/27
  • completed fcsgx workflow by @yumisims in https://github.com/sanger-tol/ascc/pull/29
  • Dp24 gc content by @DLBPointon in https://github.com/sanger-tol/ascc/pull/28
  • Githubtesting1 by @yumisims in https://github.com/sanger-tol/ascc/pull/31
  • add vecscreen test set on ci, checkin coverage related scripts, updat… by @yumisims in https://github.com/sanger-tol/ascc/pull/32
  • Dp24 barcodes by @DLBPointon in https://github.com/sanger-tol/ascc/pull/34
  • Dp24 organellar by @DLBPointon in https://github.com/sanger-tol/ascc/pull/35
  • Dp24 organellar by @DLBPointon in https://github.com/sanger-tol/ascc/pull/38
  • read depth coverage workflow by @yumisims in https://github.com/sanger-tol/ascc/pull/37
  • Dp24 vecscreen2 updates by @DLBPointon in https://github.com/sanger-tol/ascc/pull/41
  • VecScreen by @eeaunin in https://github.com/sanger-tol/ascc/pull/39
  • corrected bin/chunkassemblyfor_vecscreen.py by @yumisims in https://github.com/sanger-tol/ascc/pull/42
  • Kmer count + Dimensionality reduction by @weaglesBio in https://github.com/sanger-tol/ascc/pull/40
  • Update README.md by @DLBPointon in https://github.com/sanger-tol/ascc/pull/47
  • Edits to the dp24btkdatasets branch by @eeaunin in https://github.com/sanger-tol/ascc/pull/55
  • Many additions by @DLBPointon in https://github.com/sanger-tol/ascc/pull/48
  • Dlb pointon patch by @DLBPointon in https://github.com/sanger-tol/ascc/pull/62
  • Dev ea10 documentation. Edited documentation files by @eeaunin in https://github.com/sanger-tol/ascc/pull/59
  • ASCC multi-assembly re-write by @DLBPointon in https://github.com/sanger-tol/ascc/pull/65
  • Ability to use GZipped input by @DLBPointon in https://github.com/sanger-tol/ascc/pull/75
  • Dp24 grabfiles once by @DLBPointon in https://github.com/sanger-tol/ascc/pull/76
  • Update FCSGX module + steps improvements by @DLBPointon in https://github.com/sanger-tol/ascc/pull/74
  • edited the kmers dimensionality reduction script by @eeaunin in https://github.com/sanger-tol/ascc/pull/77
  • List and kmer enhancements by @DLBPointon in https://github.com/sanger-tol/ascc/pull/79
  • Updating many things by @DLBPointon in https://github.com/sanger-tol/ascc/pull/78
  • Significant updates to improve workflow by @DLBPointon in https://github.com/sanger-tol/ascc/pull/84
  • Removing Mapping and fixing race conditions by @DLBPointon in https://github.com/sanger-tol/ascc/pull/85
  • Dev copy by @DLBPointon in https://github.com/sanger-tol/ascc/pull/86
  • Getting ready for 0.1.0 by @DLBPointon in https://github.com/sanger-tol/ascc/pull/88
  • kmers part: bug fixes and documentation enhancements by @eeaunin in https://github.com/sanger-tol/ascc/pull/90
  • Updates for release by @DLBPointon in https://github.com/sanger-tol/ascc/pull/89
  • Dev main by @DLBPointon in https://github.com/sanger-tol/ascc/pull/92
  • Getting close to 0.1.0 by @DLBPointon in https://github.com/sanger-tol/ascc/pull/91

New Contributors

  • @DLBPointon made their first contribution in https://github.com/sanger-tol/ascc/pull/18
  • @yumisims made their first contribution in https://github.com/sanger-tol/ascc/pull/27
  • @eeaunin made their first contribution in https://github.com/sanger-tol/ascc/pull/39
  • @weaglesBio made their first contribution in https://github.com/sanger-tol/ascc/pull/40

Full Changelog: https://github.com/sanger-tol/ascc/commits/0.1.0

- Python
Published by DLBPointon over 1 year ago