toolkit - 0.4-beta Breaking new gound [2024-10-17]

Fourth beta release of nf-microbe/toolkit. Includes MAJOR restructuring and additions to pipeline. In essence, this is the first release of a new pipeline because of the deletions and restructuring that took place.

Description of changes

• #26
• All uneccessary nf-core code was removed to simplify the pipeline.
• Nested subworkflows were simplified and broken up, so subworkflows contain only one level. Many subworkflows were broken back down into individual modules.
• Assembly downloads, assembly splitting, MGE filtering, MGE dereplication, Phage host ID, MGE clustering, provirus activity, virus lifestyle, and MGE abundance functionalities were added
• pipeline nf-tests were removed. They will be added back in release 0.5-beta
• The modules repository was also updated and simplified (see here: https://github.com/nf-microbe/modules)

- Nextflow
Published by CarsonJM over 1 year ago

toolkit - v0.3.1beta - Testing grounds [2024-09-27]

Fixed

• #23 Fixed json schema URL (Fixed by @CarsonJM)

- Nextflow
Published by CarsonJM over 1 year ago

toolkit - v0.3beta - Testing grounds [2024-09-27]

v0.3beta - Testing grounds [2024-09-27]

Third beta release of nf-microbe/toolkit. Includes options for downloading SRA FastQ files, Logan assemblies, and Logan sequences processed to be input into assemblers.

Added

• #21 Added options for downloading FastQ files from SRA (sra/sratools module added by @CarsonJM)
• #21 Added options for downloading Logan assemblies (logan/contigawscli module added by @CarsonJM)
• #21 Added options for downloading and processing Logan sequences for input into assembly (logan/contigawsclimultiplier logan/unitigawsclimultiplier, accession_logan_fasta modules/subworkflows added by @CarsonJM)
• #21 rmEmptyFastQ and rmEmptyFastA modules updated, and full pipeline stub tests implemented (added by @CarsonJM)

Fixed

• #21 Fixed UW Hyak profile to retry with exitStatus 250, an out of memory error for SPAdes (Fixed by @CarsonJM)
• #21 Fixed checkv/genbankhits module erroring out when an empty file was input (Fixed by @CarsonJM)

- Nextflow
Published by CarsonJM over 1 year ago

toolkit - 0.2-beta - Stomping grounds [2024-09-24]

Added

• #17 Added assembly extension, assembly QC, MGE classification, and virus completeness (added by @CarsonJM)

Fixed

• #17 Fixed resource requests for UW Hyak to prevent over requesting resources.

- Nextflow
Published by CarsonJM over 1 year ago

toolkit - 0.1-beta - Testing grounds [2024-09-06]

v1.0beta - Testing grounds [2024-09-06]

Initial beta release of nf-microbe/toolkit for functionality testing, created with the nf-core template.

Added

• #1 Added read preprocessing functionality (added by @CarsonJM)
• #2 Added read assembly functionality (added by @CarsonJM)
• #5 Incorporated robust CI testing (added by @CarsonJM)

Fixed

Dependencies

Deprecated

- Nextflow
Published by CarsonJM almost 2 years ago