gasnomenclature - 0.8.0

0.8.0 - 2025/08/29

Added

Reduce the Number of Loci used in Analysis

• Update the PREPROCESS_REFERENCES process to use only the selected loci specified by the --pd_columns parameter. PR #80
• Update the LOCIDEX_MERGE process to include only the selected loci specified by the --pd_columns parameter in the profile.tsv file. PR #81
  • Updated locidex version to v.0.4.0 which adds a --loci parameter to input select loci for included in profile.tsv. PR #81
• Add parameter --skip_reduce_loci to skip reducing loci. PR #80

- Nextflow
Published by sgsutcliffe 10 months ago

gasnomenclature - 0.7.2

0.7.2 - 2025/08/06

Modified

• Parameter logic for PROFILE_DISTS was changed to only use --pd_max_cpus if it is below the task.cpus. PR #78
• Remove --max_mem in favor of --batch_size. PR #78

- Nextflow
Published by sgsutcliffe 11 months ago

gasnomenclature - 0.7.1

0.7.1 - 2025/08/05

Bug Fix

- Fix the bug that is caused by clusters not matching profiles issue #75. PR #76

- Nextflow
Published by sgsutcliffe 11 months ago

gasnomenclature - 0.7.0

0.7.0 - 2025/07/31

Added

• Added a PREPROCESS_PROFILES process that adds a @ prefix to the --db_profiles sample_id to force unique identifiers for samples (required for profile_dists). If reference/background profiles are already unique process can be overriden with --skip_prefix_background_profiles true. PR #72
• Made to new profile_dists parameters available to nextflow pipeline --pd_max_cpus and --pd_max_batch_size. PR #73

Modified

• APPEND_PROFILES no longer renames sample_id with duplicate to prevent conflicts for profile_dists, user should keep the default --skip_prefix_background_profiles unless they know that there is no duplicates. PR #72
• Moved the setting of non-filepath parameters for PROFILE_DISTS to the config/modules.config. PR #73

- Nextflow
Published by sgsutcliffe 11 months ago

gasnomenclature - 0.6.3

0.6.3 - 2025/07/11

Fix

• Fixed issue with csvtk cat | csvtk sort failing in APPEND_PROFILES step when working with large amounts of data. PR #70

- Nextflow
Published by apetkau 12 months ago

gasnomenclature - 0.6.2

0.6.2 - 2025/06/13

Updated

• Update profile_dists to v.1.0.8. PR #68
• Updated nf-core linting and some of the nf-core GitHub actions to the latest versions. PR #68
• Updated nf-core module custom_dumpsoftwareversions to latest version (commit 05954dab2ff481bcb999f24455da29a5828af08d). PR #68

Added

• Added an ubuntu container for the COPY_FILE process to ensure bash commands are functional. PR #68

- Nextflow
Published by sgsutcliffe about 1 year ago

gasnomenclature - 0.6.1

0.6.1 - 2025/05/26

Fix

• Fix Issue #64 by providing a new process copyFile to rename duplicate MLST files. PR #63
• Fix Issue #63 changing input type for merge_tsv. PR #63

Updated

• Update profile_dists to v.1.0.6. PR #63

- Nextflow
Published by sgsutcliffe about 1 year ago

gasnomenclature - 0.6.0

0.6.0 - 2025/05/12

Updated

• Updated profile_dists to version 1.0.5. PR #59
• Updated genomicaddressservice to version 0.2.0. PR #59
• Added software_versions.yml to pipeline output. PR #59

Fix

• A bug where addresses weren't called when no samples in the input sample sheet had addressess already assigned. PR #60
• A bug where large gzipped files would cause pipe errors (141) and then the append_profiles process would fail. This would cause the whole pipeline to fail. A fix has been added to prevent this failure from failing the process. PR #61
• Fixed issue #57, where LOCIDEX_MERGE had file collisions in pubDir due to multiple processes generating the same file name (when split into multiple batches). PR #58

- Nextflow
Published by emarinier about 1 year ago

gasnomenclature - 0.5.1

0.5.1 - 2025/05/01

Updated

• Increased resources from process_single to process_high for APPEND_PROFILES step in order to handle very large collections of background profiles. PR #55.

Fix

• Query samples now put into batches for LOCIDEX_MERGE fixing the issue #52. PR #53

- Nextflow
Published by apetkau about 1 year ago

gasnomenclature - Version 0.5.0

0.5.0 - 2025/04/02

Updated

• Update the locidex version to 0.3.0. locidex merge has integrated the functionality of module input_assure. PR 45
• Update the genomic address service version to 0.1.5. Changes how multiple samples without address are assigned addresses when belonging to the same cluster. PR 47 PR 48
• Update the profile_dist version to 1.0.4. PR 50

Enhancement

• locidex merge in 0.3.0 now performs the functionality of input_assure (checking sample name against MLST profiles). This allows gasnomenclature to remove input_assure so that the MLST JSON file is read only once, and no longer needs to re-write with correction. PR 45

Changes

• The output from locidex merge now includes a MLST_error_report.csv similar to that of input_assure (this file is also passed to concat). PR 45
• The input/output for gasnomenclature "address" has been changed to "genomicaddressname". PR 48
• Modified the UI for running the pipeline in IRIDA-Next web interface. PR 50

- Nextflow
Published by sgsutcliffe about 1 year ago

gasnomenclature - Version 0.4.0

0.4.0 - 2025/03/03

Enhancement

• 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

Updated

• The container for docker/singularity for Profile_Dist was changed to quay.io/biocontainer build 1.0.3 (this profile_dists version was just to fix the PYPI build recipe which caused the container to not be built) which has no changes from 1.0.2

- Nextflow
Published by sgsutcliffe over 1 year ago

gasnomenclature - Version 0.3.1

0.3.1 - 2025/02/11

Fixed

• Addressed the pipefail Issue #36 when large sample sizes are passed to APPEND_CLUSTERS() in PR #37 by replacing a pipe with a temporary intermediate file.
• Updated GAS to version 0.1.4 which resolves Issue #38 and #33 which now allows linkage.method parameters of gasnomenclature to be passed to GAS call.

- Nextflow
Published by sgsutcliffe over 1 year ago

gasnomenclature - Version 0.3.0

0.3.0 - 2025/01/09

Added

• Enhanced the pipeline to integrate optional user-provided reference profiles and cluster addresses for additional samples PR #29:
  • Added support for --db_profiles via the APPEND_PROFILES process
  • Added support for --db_clusters via the APPEND_CLUSTERS process

• Added tests to verify the additional databases can be incorporated and that both databases are required together for their respective processes.

• Added the ability to include a sample_name column in the input samplesheet.csv. Allows for compatibility with IRIDA-Next input configuration PR #30:

  • sample_name special characters will be replaced with "_"
  • If no sample_name is supplied in the column sample will be used
  • To avoid repeat values for sample_name all sample_name values will be suffixed with the unique sample value from the input file

• Updated gas/call to version 0.1.2 and both CLUSTER_FILE and APPEND_CLUSTERS to comply with the latest formatting requirements.

Changed

• Genomic Service Address version 0.1.1 -> 0.1.3

• Refined the format of reference_cluster.tsv (rclusters) used by GAS CALL to require only id and address columns. This change involved updates to both the append_clusters and cluster_file modules.

- Nextflow
Published by sgsutcliffe over 1 year ago

gasnomenclature - Version 0.2.3

0.2.3 - 2024/09/25

Changed

• Updated FILTER_QUERY process to treat query_ids as a file input (path instead of val) for proper file path handling across environments PR27
• Addressed Issue26

- Nextflow
Published by kylacochrane over 1 year ago

gasnomenclature - Version 0.2.2

0.2.2 - 2024/09/13

Changed

• Updated FILTER_QUERY to process query IDs from a file rather than passing them as a string, preventing errors caused by long argument strings PR24

- Nextflow
Published by kylacochrane almost 2 years ago

gasnomenclature - Version 0.2.1

0.2.1 - 2024/09/10

Changed

• Upgraded profile_dists to version 1.0.2 in the container closure

- Nextflow
Published by kylacochrane almost 2 years ago

gasnomenclature - Version 0.2.0

0.2.0 - 2024/09/05

Changed

• Upgraded locidex/merge to version 0.2.3 and updated input_assure.py and test data for compatibility with the new mlst.json allele file format PR20
• Removed quay.io docker repository tags from modules PR19

This pipeline is now compatible only with output generated by Locidex v0.2.3+ and Mikrokondo v0.4.0+.

- Nextflow
Published by kylacochrane almost 2 years ago

gasnomenclature - Version 0.1.0

0.1.0 - 2024-06-28

Added

• Input of cg/wgMLST allele calls produced from locidex.
• Output of assigned cluster addresses for any query samples using profile_dists and gas call.

- Nextflow
Published by kylacochrane almost 2 years ago