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