Releases: cidgoh/nf-ncov-voc
Releases · cidgoh/nf-ncov-voc
v1.3.0
What's Changed
- Complete support for Mpox
- Complete support for wastewater samples
- Enabling additional functional annotation using the data specs
- Integration of Data Harmonizer template for verifying the annotation
- Integrated Ontologized terms for functional annotation
- A complete mutation index generated for each run with the capability of updating previous
Details
- enable wastewater vcf processing by @miseminger in #129
- parse ao/ro/dp based on variant calling source by @miseminger in #130
- enable find_sample_size() for wastewater data by @miseminger in #131
- Separate functional annotation and variant info into new scripts by @miseminger in #133
- Wastewater sample size & splitnames changes by @miseminger in #136
- workaround if gene_positions.json doesn't have protein coordinates yet by @miseminger in #137
- add gff2json.py, allow filename for mutations not matched with Pokay by @miseminger in #138
- Add alias names to GVFs by @miseminger in #139
- Upload logfile creation + index updating script, and add aliases to the Pokay annotations file by @miseminger in #140
- Update vcf2gvf.py to work with new gene positions JSON format by @miseminger in #143
- switch to list of GVFs as input by @miseminger in #145
- VCF 'INFO' parsing error + functional annotation merge fix by @miseminger in #146
- Fix missing alias names bug by @miseminger in #147
- Merging dev to master by @anwarMZ in #148
- Add HGVS names to GVFs and mutation index by @miseminger in #149
- Solve code-stopping HGVS naming bug by @miseminger in #154
- split update_index_and_logfile.py into 3 scripts, and use Dask by @miseminger in #155
- Use spec format for functional annotation, add new pragmas to GVFs by @miseminger in #156
- Merging dev to master by @anwarMZ in #157
- viral genomes by @anwarMZ in #158
- make sure all empty key pairs are written as "attribute_key=n/a" by @miseminger in #160
- add missing regex parameter in functions.py by @miseminger in #161
- Make addfunctions2gvf.py compatible with new 'n/a' in "comb_mutation" and 'multiaa_comb_mutation' columns by @miseminger in #163
- get sample_size from any row in sample_stats for user-uploaded fasta by @miseminger in #164
- Some fixes for Conda by @ivansg44 in #169
- Merging development to master by @anwarMZ in #171
- update docker containers for local modules by @anwarMZ in #172
- update default docker.registry by @anwarMZ in #173
- updated docker registry by @anwarMZ in #174
- Development by @anwarMZ in #175
- Development by @anwarMZ in #176
- Adapt to new DH template by @miseminger in #184
- Remove duplicate rows in functional annotation file by @miseminger in #187
- Add MPOX functional annotation file by @miseminger in #186
- Fix duplication bug and quotation marks issue by @miseminger in #188
- Fix missing file and alias names by @miseminger in #189
- vcf2gvf.py error fixing by @miseminger in #190
- regex fix, index column name change by @miseminger in #191
- Fix unequal length lists by @miseminger in #192
- fix dtypes in merge_indices by @miseminger in #193
- Merge dev to master by @anwarMZ in #194
- Merging new changes to master from development branch by @anwarMZ in #197
New Contributors
Full Changelog: v1.2.1...v1.3.0
Contributors
anwarMZ, miseminger, and ivansg44
Assets 2
nf-ncov-voc-1.2.1
What's Changed
Updated GVF format to have a row for each mutation and alternate allele with respective functions.
Full Changelog: v1.2.0...v1.2.1
nf-ncov-voc-1.2.0
What's Changed
- Update omicron sub-variants by @anwarMZ in #99
- Update variants_who.tsv by @anwarMZ in #104
- Updating list of variants, omicron sub-lineages and metadata headers by @anwarMZ in #105
- Update vcf2gvf.py by @anwarMZ in #106
- Update vcf2gvf.py by @anwarMZ in #107
- parse constellations file for gene and protein names; who_variants.ts… by @miseminger in #109
- Merging dev branch into master by @anwarMZ in #110
- Fix issue of functions not adding by @miseminger in #111
- Development by @anwarMZ in #112
- Enable parsing of new who variants file by @miseminger in #113
- merge dev branch by @anwarMZ in #114
- update main.nf for user mode by @anwarMZ in #115
- Update vcf2gvf.py by @anwarMZ in #116
- XBB.1.5 updates by @anwarMZ in #117
- Madeline dev by @miseminger in #118
- fix missing clade_file issue for user mode by @miseminger in #119
- fix sample_size type bug by @miseminger in #120
- add missing attributes from INFO back in by @miseminger in #121
- Split relevant SNPeff annotations into separate rows by @miseminger in #122
- Remove unwanted SNPeff annotations by @miseminger in #124
- updating dev features and reference genomes by @anwarMZ in #126
- Take same number of annotations as there are AO values by @miseminger in #127
Full Changelog: v1.1.0...v1.2.0
Contributors
anwarMZ and miseminger
Assets 2
nf-ncov-voc-1.1.0
Contributors
anwarMZ
Assets 2
nf-ncov-voc-1.0.0
What's Changed
- Increasing reproducibility by creating DOCKERFILE and Singularity Recipe by @anwarMZ in #37
- Updating Documentation by @anwarMZ in #39
- clade_defining status based on threshold by @miseminger in #35
- Adding documentation for parameters and citations by @anwarMZ in #40
- Work with single-line variants_who.tsv format, workaround comma-containing 'ao' columns by @miseminger in #41
- Fixed "ValueError: 1 is not in range" error by @miseminger in #42
- add num_seqs attribute to gvf by @miseminger in #44
- Update variants 2021-10-29 by @anwarMZ in #48
- Update variants - 30 October by @anwarMZ in #49
- Fixing the empty file bug if no sequence passes QC module by @anwarMZ in #50
- renaming workflow configuration files by @anwarMZ in #51
- include parse_sample_size.py by @miseminger in #46
- Workflow reading when it a file has single genome by @anwarMZ in #53
- Update parse_variants.py by @anwarMZ in #54
- Update main.nf by @anwarMZ in #55
- Updating minimal error by @anwarMZ in #56
- Cleaning scripts up by @anwarMZ in #57
- Updating VCF->GVF module by @anwarMZ in #58
- SEQKITSTATS update for collated stats by @anwarMZ in #59
- Update, parameters, functions & PEP 8 formatting by @anwarMZ in #60
- Update issue templates by @anwarMZ in #62
- Update issue templates by @anwarMZ in #61
- Adding Surveillance reports feature and Mapping VirusSeq data to Pangolin lineages by @anwarMZ in #65
- Updating parameters in a markdown file for reference and replacing direct values with parameter variables in the processes by @anwarMZ in #66
- Adding resource definitions in resources.config and assigning dev_env as default label by @anwarMZ in #67
- Adding CIDGOH and nf-ncov-voc header by @anwarMZ in #68
- Update nextflow.config for improved reproducibility and resource by @anwarMZ in #69
- Adding Omicron as a new VOC (26-Nov-2021) by @anwarMZ in #70
- Adding Omicron as a new VOC (26-Nov-2021) by @anwarMZ in #71
- Create surveillance_report_description.md by @anwarMZ in #72
- Madeline by @miseminger in #73
- get sample_size from function, remove sample_size and variant_pop_siz… by @miseminger in #74
- Update variants_who.tsv by @anwarMZ in #75
- 'sample_collection_date' based filtering enabled in extract_metadata.py by @anwarMZ in #77
- Restructured modules to allow nf-core modules by @anwarMZ in #79
- Integrating pangolin module from nf-core by @anwarMZ in #80
- Restructured required files by @anwarMZ in #82
- Updated scripts for reproducibility by @anwarMZ in #83
- New Feature: Summarized Surveillance report - PDF by @anwarMZ in #85
- Restructured workflows for better integration with different file formats by @anwarMZ in #86
- Updated dataflow workflow for nf-ncov-voc by @anwarMZ in #87
- Updating bits and pieces by @anwarMZ in #88
- Update .gitignore by @anwarMZ in #89
- change to allow user-uploaded files by @miseminger in #90
- Updating structure for mode=user to produce surveillance reports for user uploaded files through covidmvp by @anwarMZ in #91
- Update README.md by @anwarMZ in #92
- Replacing xelatex with conda wrapped techtonic by @anwarMZ in #93
Full Changelog: v0.1.1...v1.0.0
Contributors
anwarMZ and miseminger
Assets 2
nf-ncov-voc-0.1.1
What's Changed
- Updated script to accommodate new structure of parsing variants by @anwarMZ in #34
- unknown strains, elementwise addition of counts for heterozygous mutations, hopeful bug fix by @miseminger in #32
Full Changelog: v0.1.0...v0.1.1
Contributors
anwarMZ and miseminger
Assets 2
nf-ncov-voc-0.1.0
What's Changed
- Create LICENSE by @anwarMZ in #1
- Madeline by @miseminger in #2
- Madeline by @miseminger in #3
- Madeline by @miseminger in #4
- get correct ao, ro from latest vcf by @miseminger in #5
- Update Metadata Extraction for GISAID + non GISAID table by @anwarMZ in #11
- Updated extractMetadata.py module by @anwarMZ in #12
- Remove extra files by @anwarMZ in #13
- Update custom.nf by @anwarMZ in #14
- Create functional_annotation.py by @Anoosha-Sehar in #18
- Single genome option, merging lineages into variants, reformatting mutations by @miseminger in #19
- User uploaded data (vcf, tsv, fasta) by @anwarMZ in #15
- Updating single genome option & stable version of DSL=2 in COVID MVP by @anwarMZ in #22
- Updating configurations & functional annotation version by @anwarMZ in #23
- Updating modules to reflect consistent filenames and tags by @anwarMZ in #25
- Update .gitignore by @anwarMZ in #26
- Delete definitions.py by @anwarMZ in #27
- Update main.nf by @anwarMZ in #29
- Updating workflows to DSL=2 stable version by @anwarMZ in #30
- Madeline by @miseminger in #31
New Contributors
- @anwarMZ made their first contribution in #1
- @miseminger made their first contribution in #2
- @Anoosha-Sehar made their first contribution in #18
Full Changelog: https://github.com/cidgoh/nf-ncov-voc/commits/v0.1.0
Contributors
anwarMZ, miseminger, and Anoosha-Sehar