Skip to content

ViroConstrictor v1.0.0
Compare
Choose a tag to compare
@github-actions github-actions released this 14 Apr 15:20
v1.0.0
5d0eb3b
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

⚠ BREAKING CHANGES

  • Use a single coverage level during analysis, defaults to 30 (6d6fc01)
  • add support for per-sample analysis settings with an input samplesheet in Excel, TSV or CSV format (a0b726)
  • Add support for BED files in amplicon_covs (ece3dfa)
  • Use BED files as output of AmpliGone (79fd23)
  • Update to python version 3.10 in base environments. (minimal required version = 3.8) (184328)
  • Use a single coverage level for TrueConsense (e5701b9a)

Features

  • flexible snakemake rule_all based on samplesheet inputs (93ad0c)
  • use the snakemake Paramspace for wildcard generation (94d1738)
  • Add remove_adapters_p1 to all (64c9069)
  • Add remove_adapters_p2 and qc_filter to all (a89560)
  • Add prepare_primers (6dc7c9)
  • Add prepare_gff rule (a0bc0fb)
  • Re-add ampligone (89cc2a0)
  • Re-add qc_post to multiqc (45c0d12)
  • Re-add TrueConsense (44f36c1)
  • Re-add concat_seq (ab229de)
  • Re-add tsv output (5bf10aa)
  • Re-add breadth of coverage to snakefile (003b2f)
  • Re-add amplicon_cov (6f6088)
  • Correctly handle missing inputs in samplesheet (aa6995)
  • re-add illumina support in new workflow structure (8eb400)
  • add fastP stats to multiqc report (19627f)

Bug Fixes

  • Add option to not give primers on cli (e4c054c)
  • Check combination of samplesheet and cli args (e4c054c)
  • Fix broken snakefile (a704c5e)
  • Add .bed as filetype for primers (f16556)
  • Make prodigal and prepare_gff unique (761337)
  • Fix aggregation outputs to rule all (2269340)
  • Fix restructuring of results folder (76fda46)
  • group concatenated files in correct results subfolders (f3f1d9e)
  • Make sure all post_qc is added in multiqc (b51f0ce)
  • Remove excess bracket in various log&bench rules (4a5e96c)
  • add logs for calculate_amplicon_cov rule (fbd2c1c)
  • always use absolute path for input reference, primer and features files (fa68a7a)
  • always provide absolute path for input fastq files (0303244)
  • Raise error if fasta contains invalid char (5209a7b)
  • Bump minimum snakemake version (a31b503)
  • change multiqc memory requirements to 'high' (05b9db3)
  • filter input primer bedfile to only output matching refID bedfile (c2b9c0c)

Code Refactoring

  • move version to init file (e4c054c)
  • Remove empty.primers (bfe0044)
  • use the snakemake Paramspace wildcards in the multiQC aggregation (1204b09)
  • add the "extract_refs.py" script to repo (5a7ea4)
  • move multiqc input function to top of snakefile (1134bb)
  • use new prepare_primers rule in new structure (4d06939)
  • use new prepare_gffs rule with the new structure (537d09)
  • add basic gff filter script (09ada9)
  • Refactor with bottum up approach (682cafa)
  • Rename Sample to sample (a6c0e48)
  • Change to wc_pattern (214e21)
  • Switch wc_pattern to wc_folder (40d4d2e)
  • Remove threads: 1 as it is default (5cd6ca6)
  • Make wildcard notation consistent (8fe4f7e)
  • Re-ordering of code (b3d891)
  • Remove mincov variable in snakefile (5bb47a9)
  • change used fonts in the generated report to accomodate fpdf2 (5bb91d1)
  • merge if statement blocks to singular condition (7b2882f)
  • simplify boolean returns (615d2cf)
  • use new expression for conditional in samplesheet generator (8ca585a)

Dependencies

  • update AmpliGone to version 1.0.1 (e4c054c)
  • update TrueConsense version to v0.4.0 (e4c054c)
  • use Pypi for AmpliGone installation instead of building from source (e4c054c)
  • add python3.7 to the Alignment env for improved env-stability (d87c746)
  • update snakemake to lenient version 7.3 (56d8fe)

Documentation

  • Add information for primer bed support (e4c054c)
  • update docs for multi-target analysis (e4c054c)
  • update documentation for new ViroConstrictor functions (e4c054c)
  • update installation command for python3.10 (e4c054c)
  • update documentation index page with correct required snakemake version (e4c054c)
  • Add explanatory docstring to CheckSampleProperties function (4a552ad)
  • Add explanatory docstrings to all functions in ViroConstrictor.parser (b09f4d)
  • Add explanatory docstrings to all functions in ViroConstrictor.runconfigs (2ff8185)
  • Add explanatory docstrings to all functions in ViroConstrictor.samplesheet (a1e7093)
  • Add explanatory docstrings to all functions in ViroConstrictor.userprofile (30ec8af8)
  • Add explanatory docstrings to all functions in ViroConstrictor.validatefasta (c199d7c9)
  • Add error message for samplesheet duplicates (efa0761)
Assets 2
Loading