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Merge dev to master#194

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anwarMZ merged 171 commits intomastercidgoh/nf-ncov-voc:masterfrom developmentcidgoh/nf-ncov-voc:developmentCopy head branch name to clipboardDec 16, 2024

+19,807-5,277

Commits

Commits on Apr 29, 2024

• make JSON file required in vcf2gvf.py

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• add new attribute, 'transcript_id', using locus_tag from JSON

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• add transcript_id in parentheses for HGVS nt names

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• get rid of UserWarning for match groups

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• remove unused imports

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• include alias_protein_id in HGVS alias names, and make a new attribute called 'alias_protein_id'

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• update nt_delins_regex

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Commits on Apr 30, 2024

• add new attribute, 'gene_symbol', from 'gene' in the JSON file

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• add 'gene_symbol' and 'protein_symbol' columns to mutation index

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• rename 'gene' column in mutation index to 'gene_name'

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• change 'protein symbol' column name to 'gene name' to match GVF and mutation index; remove need for JSON file

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• change 'protein symbol' column in df made from Pokay repo to 'gene name' to allow merge with mutation index

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Commits on Jul 30, 2024

• change 'gene' attribute to 'gene_name' in VCF

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• change 'gene' to 'gene_name' and add 'gene_symbol'

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• make all args required for log and index creation

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• update column names to match DH template, make mutation index optional

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• fix formatting for non-index file

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• merge dfs on 'protein symbol' instead

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• sort by nucleotide position

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• update for new functional annotation format

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• update to match new functional annotation format

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• rename 'alias_protein' to 'mat_pep'

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Commits on Aug 8, 2024

• add Pokay names as 'pokay_id'

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• add missing 'pokay_id' for ORF8

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Commits on Sep 15, 2024

• Add script

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• Add SARS-CoV-2 ontology terms JSONs

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• Delete unwanted files

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Commits on Sep 16, 2024

• upload script

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• update comment

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Commits on Sep 17, 2024

• Add ontology terms to JSON, and remove pokay_id

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  8955e30

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• add aliases from Sept 9 issue

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• remove alias names that are the same as the gene name

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Commits on Sep 18, 2024

• Temporarily add Pokay name for PLpro to aliases

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• Add RdRp back in to alias list

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• Add protein_alias lists manually

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• Add ontology terms to functional annotation file

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• Update column names to match template

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• Don't merge on mat_pep anymore

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• add BioRegistry prefix for doi

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Commits on Sep 19, 2024

• Add MPOX ROBOT table

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Commits on Sep 27, 2024

• update for MPOX

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  bd967d5

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• Add ontology term JSONs for MPOX

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Commits on Oct 1, 2024

• Add strand orientation for MPOX

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• add gene and strand orientation for MPOX

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  5166d9e

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• make code useful for SC2 or MPOX

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  9a53e60

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• Update SARS-CoV-2 JSONs with gene and strand orientations:

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  2c62b20

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• Add gene and strand orientation

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• Add new functional annotation file

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Commits on Oct 4, 2024

• add gene and strand orientation for MPOX, and change unknown publication status from 'false' to empty string

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• add MPOX functional annotations in DH template format

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Commits on Oct 22, 2024

• remove mutation index rows that don't have a nucleotide mutation

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• use pd.explode() in unnest_multi()

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• workaround unmatched list lengths to work with pd.explode()

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  48d068f

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Commits on Oct 23, 2024

• Adapt vcf2gvf to new JSON keys

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Commits on Oct 24, 2024

• align attribute keys with DH template

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• align attribute keys with DH template

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• adapt to new JSON keys

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• archive copy of gvf2tsv.py

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• Produce 1 TSV from GVF, ignoring clades

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• Update to match new GVF keys

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• add gene_orientation and strand_orientation to gvf

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  ac59ae3

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• change VP37 to be alias of OPG057 protein, and add to JSON

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• remove VP37 mentions from MPXVgp025

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• add protein_alias key to all CDS entries

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• add indent to fix bug

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• replace 'pokay' with 'template' for generalizability

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• Rename functional annotation script

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• take 'doi:' off saved dois

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Commits on Oct 25, 2024

• add definitely the latest version

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• match new DH format

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• Delete assets/virus_functionalAnnotation/NC_045512.2/Pokay_functionalAnnotation_SARSCoV2_v1.0.tsv

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• Delete assets/virus_functionalAnnotation/NC_045512.2/Pokay_functionalAnnotation_SARSCoV2_v2.0.tsv

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• add 'clade' argument and attribute

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  4be0584

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• Merge branch 'madeline-1' of github.com:cidgoh/nf-ncov-voc into madeline-1

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• add 'functional_annotation_resource' attribute

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• add functional annotation columns as GVF attributes

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• change 'measured_variant_functional_effect_description' attribute to 'variant_functional_effect_description'

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• adapt to new DH template format

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• update column names

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• Merge pull request #184 from cidgoh/madeline-1

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Commits on Oct 28, 2024

• catch MPOX genes and proteins

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• catch MPOX URLs

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• upload MPOX functional annotation file

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  86f9d3c

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• add 'pmid:' prefix

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• add 'pmid:' prefix

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• Delete assets/virus_functionalAnnotation/NC_063383.1/pokay_annotations_v_0.1.tsv

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• Delete assets/virus_functionalAnnotation/NC_063383.1/pokay_annotations_v_0.2.tsv

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Commits on Oct 29, 2024

• fixed typos

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Commits on Nov 8, 2024

• solve duplicated rows bug

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• remove troubleshooting print statement

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• remove duplicate rows

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Commits on Nov 11, 2024

• Merge pull request #187 from cidgoh/madeline-2

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Commits on Nov 12, 2024

• Merge pull request #186 from cidgoh/madeline

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Commits on Nov 13, 2024

• solve duplication issue

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• solve extra quotes issue

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• add updated functional annotation file

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  1c2cd51

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• Delete assets/virus_functionalAnnotation/NC_045512.2/Pokay_functionalAnnotation_SARSCoV2_v3.0.tsv

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• ensure PMIDs are integers

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• add PMIDs to functional annotation file

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• Delete assets/virus_functionalAnnotation/NC_045512.2/Pokay_functionalAnnotation_SARSCoV2_v4.0.tsv

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• Merge pull request #188 from cidgoh/madeline-1

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Commits on Nov 15, 2024

• update Mpox workflow

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• updated configuration workflow

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• updated configurations

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• updated README

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• updated SARS-CoV-2 workflow

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• updated main workflow file

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• updated ViralAi module

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• updated annotation sub-workflow

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• updated ignored files

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• added vscode plugins

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Commits on Nov 16, 2024

• updated nextflow formatting

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• updated main.nf structure

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• updated main.nf structure

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• updated main.nf structure

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• updated main.nf structure

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Commits on Nov 26, 2024

• fix missing file

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• try fixing 'alias' missing key

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• updated config

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• updated subworkflows

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• updated subworkflows

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• updated modules

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• updated main file

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• updated workflows file

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• updated nextflow config

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• vscode nextflow extension

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• Merge pull request #189 from cidgoh/mri

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Commits on Nov 28, 2024

• fix 'Pl_pro' alias error

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• Merge pull request #190 from cidgoh/mri_27

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Commits on Nov 29, 2024

• Make all index column names lowercase

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• comment out index row removal before merge

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• capture mat_pep_acc from VCF

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• Merge pull request #191 from cidgoh/madeline

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• fix all relevant unequal length columns by adding nans

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• Merge pull request #192 from cidgoh/madeline

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Commits on Dec 9, 2024

• update scripts

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• updated conf

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• updated sub-workflows

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• updated sars-cov-2 workflow

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• updated preset param files

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• updated tsv2pdf module

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• version bump for pokay sars-cov-2

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• updated output files to match gvf naming

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• update sars-cov-2 test data

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Commits on Dec 10, 2024

• update sars-cov-2 test data

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Commits on Dec 13, 2024

• updated covidmvp workflow

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• updated subworkflows

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• updated and formatted modules

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• updated merge_indices

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• update dtypes to match index columns

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• update index column names

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• Merge pull request #193 from cidgoh/madeline3

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• archived script

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Commits on Dec 15, 2024

• updated config

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• fixed covidmvp user uploaded error

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• updated user uploaded test

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• updated preprocessing

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Commits on Dec 16, 2024

• updated github actions testing

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• fixed actions typo

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• updated relative path to seq file

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• updated workflow params and conf

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• updated test data for reference

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• updated test data

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• update module docker containers

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• update containers

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• update workflow

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• update workflow singularity

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• update containers

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• updated for master

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