fastmatchirida - 0.4.0-pnc1

0.4.0-pnc1 - 2025-08-20

Changed

• Changed calc_source_category to calc_source_type. PR 32

- Nextflow
Published by emarinier 10 months ago

fastmatchirida - 0.4.0-pnc0

0.4.0-pnc0 - 2025-08-13

Added

• A PNC-customized branch of the FastMatch pipeline with specific metadata fields and parameters tailored to PNC requirements. PR 30

- Nextflow
Published by emarinier 10 months ago

fastmatchirida - 0.4.0

0.4.0 - 2025-08-11

Changed

• The number of metadata columns in the sample sheet has been increased from 8 to 16. PR 28

- Nextflow
Published by emarinier 10 months ago

fastmatchirida - 0.3.3

0.3.3 - 2025-06-12

Updated

• Update profile_dists to v.1.0.8. PR 25
• Updated nf-core linting and some of the nf-core GitHub actions to the latest versions. PR 25
• Updated nf-core module custom_dumpsoftwareversions to latest version (commit 05954dab2ff481bcb999f24455da29a5828af08d). PR 25

Added

• Added an ubuntu container for the COPY_FILE process to ensure bash commands are functional. PR 26

- Nextflow
Published by sgsutcliffe 12 months ago

fastmatchirida - 0.3.2

0.3.2 - 2025-05-23

• Added baseName to the check for repeat MLST allele files (in case file paths are different). PR 22

- Nextflow
Published by sgsutcliffe about 1 year ago

fastmatchirida - 0.3.1

0.3.1 - 2025-05-23

Fixes

• Fix Issue #19 by providing a new process copyFile to rename duplicate MLST files. PR 18
• Fix Issue #18 changing input type for merge_tsv. PR 18

Updated

• Update profile_dists to v.1.0.6. PR 18

- Nextflow
Published by sgsutcliffe about 1 year ago

fastmatchirida - 0.3.0

0.3.0 - 2025-05-08

Update

• Update profile_dists to 1.0.5. PR 14
• Update the locidex version to 0.3.0. locidex merge has integrated the functionality of module input_assure. PR 15

Add

• Add software_versions.yml to iridanext.output.json.gz global files. PR 14

Changed

• Change the default profile_dists default setting pd_skip = true. PR 16

Enhancement

• locidex merge in 0.3.0 now performs the functionality of input_assure (checking sample name against MLST profiles). This allows fastmatchirida to remove input_assure so that the MLST JSON file is read only once, and no longer needs to re-write with correction. PR 15
• Added a pre-processing step to the input of LOCIDEX_MERGE that splits-up samples, into batches (default batch size: 100), to allow for LOCIDEX_MERGE to be run in parallel. To modify the size of batches use the parameter --batch_size n. PR 15

- Nextflow
Published by sgsutcliffe about 1 year ago

fastmatchirida - 0.2.0

0.2.0 - 2025-04-09

Changed

• Changed file extensions (.text -> .tsv) of output files from GAS_MCLUSTER and PROFILE_DISTS found in the iridanext.output.json. Output files are now compatiable with file preview feature in IRIDA Next. PR 10
• Changed the default threshold for minimum matching alleles from 1 to 50 for filtering. The idea being to show more results and let user filter themselves after. PR 12

Updated

- Update the profile_dist version to 1.0.4. PR 11

- Nextflow
Published by sgsutcliffe about 1 year ago

fastmatchirida - 0.1.1

[0.1.1] - 2024-01-17

This release improves documentation and testing.

- Nextflow
Published by emarinier over 1 year ago

fastmatchirida - 0.1.0 Release

0.1.0 - 2024-12-13

Release

fastmatchirida is built using gasclustering 0.4.0 as a template. The goal of the release is to set up the basic-functionality of the pipeline for testing in IRIDA-Next.

Pipeline Description

The pipline will be used, integrated into IRIDA-Next, to allow users to select reference samples that meet with a minimum threshold distance to a query set of samples for downstream analysis. The output is a table (tsv and excel) of the samples that match the minium threshold distance.

- Nextflow
Published by sgsutcliffe over 1 year ago