Changelog¶

1.4.6 (2024-10-08)¶

Bug Fixes¶

properly solve DAG workflow for nonsegmented matched-ref samples (02a821a)

1.4.5 (2024-09-25)¶

Bug Fixes¶

incorrect renaming of matched references in non-segmented mode (c42740e)

1.4.4 (2024-09-16)¶

Bug Fixes¶

remove intel channel from selfupdater repositories (43fe508)

Dependencies¶

reorder and add details to the conda dependency files for compatibility with strict_channel_priority in conda config (dc9b993)

1.4.3 (2024-07-03)¶

Dependencies¶

Remove 'intel' channel from conda environments (a2e918a)

1.4.2 (2024-04-03)¶

Dependencies¶

update AmpliGone to version 1.3.1 (b6a92c8)

1.4.1 (2024-03-22)¶

Bug Fixes¶

resolve pandas FutureWarning for integer casting on a series with a single element (bb76d06)

Dependencies¶

update AmpliGone to version 1.3.0 (6f28568)
update python and pysam version in Consensus conda environment (18e4ffb)

1.4.0 (2023-09-18)¶

Features¶

add "NONE" input for primers and gff's support to the match_ref process (1581c78)
add all the match_ref analysis scripts (1581c78)
add the match_ref snakemake workflow (1581c78)
add the match_reference process (1581c78)
only initiate the match_ref wrapping process whenever it is set on the commandline or through the samplesheet (1581c78)

Bug Fixes¶

add fix for unformatted printed message (98386c1)
enforce a "None" string instead of a Nonetype used for reference prep (f4f7490)
ensure "match-ref" and "segmented" columns are always added to samplesheet (98386c1)
ensure a string value like "NA" will not be interpreted as NaN in pandas.read_csv() (ecaca5e)
pad the number in primer names in the amplicon_coverages script so the amplicons are sorted correctly (cab3a8c)
solve index out of range bug in amplicon_coverages script (ca95a8a)
suppress the strict-channel-priorities logmessage from snakemake (1654891)
workaround to make sure the found segments can properly be 'exploded' in the resulting dataframe (9db4a42)

Dependencies¶

remove anaconda channel from selfupdating method (3db1cfb)
remove the anaconda and defaults channels as providers in conda environment recipes, set nodefaults (08ed236)
replace gffpandas in script to AminoExtract functions (599da1f)
update AminoExtract to version 0.3.1 (08e4a22)
use a forked/patched version of gffpandas instead of the pypi version (circumvent a bug in the original repo) (08e4a22)

Documentation¶

update the documentation site to represent the new match-ref and segmented arguments both on commandline and and in samplesheet (94c5ca0)
updated docstring for function check_samplesheet_rows() (98386c1)

1.3.1 (2023-05-26)¶

Bug Fixes¶

enforce absolute paths for files given through the samplesheet (40889bf)

Dependencies¶

use only snakemake-minimal as workaround for protobuf error in py3.11 (47c70db)

1.3.0 (2023-05-03)¶

Features¶

addition of proper logging functionality for the ViroConstrictor package (20a952b)
replace snakemake logging output through our own log handler for unified output (20a952b)

Bug Fixes¶

always use the absolute path of given files when parsing from the commandline options (a5b56e5)
change certainty values of match_preset_name() function to be explicitly floating points to ensure correct datatypes in downstream check (a74249c)
change preset fallback certainty threshold to be slightly more conservative (7542c46)
clean-handling of mamba solver mismatching (i.e. CDN mismatch with upstream) (680730b)
ensure variables for preset-warning fallbacks are properly set when no fallbackwarnings have to be logged (d7ddf0a)
print the sample key instead of dictionary contents in non-existing reference error log (f8c7a12)
Properly show all preset-fallback warnings instead of just the first in the index (48662db)
suppress snakemake logging output (workaround for https://github.com/snakemake/snakemake/issues/2089) (20a952b)
ensure samples_df and samples_dict always contain the same information (20a952b)

Documentation¶

add citation and DOI information to readme and documentation site (a2cf117)
add explanatory docstrings to various functions (0e1a368)
fix typo in installation docs (acc30d9)
update documentation with dedicated page for presets (7b2a66f)
updated manual with links to more detailed presets functionality explanation page (7b2a66f)
updated mkdocs configuration to include new page (7b2a66f)
updated mkdocs configuration to include the direct copy-button for code blocks (7b2a66f)

Code Refactoring¶

Use a generic (__main__.py) top level entry-point instead of the named ViroConstrictor.py entrypoint (20a952b)
re-structure argument parsing functionalities into its own class (20a952b)
re-structure snakemake run-information and config functionalities into its own class (20a952b)
remove old shell stdout-coloring method with the rich library (20a952b)
simplify several functions to ensure a properly defined return (20a952b)
Use f-strings more consistently for i.e. string concatenation with variables (20a952b)
add type-hints to all functions (20a952b)

Miscellaneous Chores¶

empty commit (84a34b9)

Dependencies¶

change biopython version to 1.81 (6bd437a)
change openpyxl version to 3.1.* (6bd437a)
change pandas version to 2.0.* (6bd437a)
change snakemake version to 7.25.* in base environment (6bd437a)
change urllib3 version to be more lenient (1.26.*) (6bd437a)
pin AminoExtract version to 0.2.1 (6bd437a)
use more lenient package requirements in setup.py to allow for both py3.10 and py3.11 builds (944f39d)

1.2.6 (2023-03-16)¶

Bug Fixes¶

add amino-acid names as a tuple to allow for hashing (9f002c7)

Dependencies¶

allow for more lenient snakemake versioning >=7.15.2 in base environment (adc6051)

1.2.5 (2023-03-14)¶

Dependencies¶

update AmpliGone to version 1.2.1 (7abaedd)
update minimal mamba version to 1.0.0 (7ad5fe8)

Documentation¶

add information badges to readme (53e818f)
update installation instructions in docs (da57e82)

1.2.4 (2023-03-02)¶

Dependencies¶

use conda for installing aminoextract instead of pip (1855470)

1.2.3 (2023-03-01)¶

Bug Fixes¶

allow input fastq files that contain multiple dots (07994a2)
ensure compability between the Influenza preset and illumina short read data (9a9f1d9)
ensure match_preset_name() actually returns all required values (d49f238)
update permissions for GH-actions workflows (1f760ba)

Documentation¶

add citations file (1f760ba)
update installation instructions for new environment file and environment creation with Mamba (84183a7)

Dependencies¶

add python-magic version 0.4.27 to environment (84183a7)
pin version of AminoExtract to 0.2.1 (84183a7)

1.2.2 (2023-01-24)¶

Bug Fixes¶

correctly parse presets when using a samplesheet (2ca2149)
make the ViroConstrictor main entrypoint less case sensitive (43b27aa)

1.2.1 (2023-01-19)¶

Bug Fixes¶

correction in argument parser to avoid a NoneType AttributeError when all required information is passed through commandline options (f2acedf)

Dependencies¶

correct the rich version in all base environment files (f2acedf)

1.2.0 (2023-01-18)¶

Features¶

add option to filted for minimum aligned length in clipper.py (d06caf5)
add option to filter spliced reads in clipper.py (d06caf5)
add support for working with presets for specific viral targets (29bfa3c)

Bug Fixes¶

add .gff3 file extension as allowed to features flag (b4fdf5d)
change Clipper settings to a per-platform config per preset (3d952bb)
change the minimal alignment length in clipper.py to be a percentage of the reference length (68597e8)
correct minimum aligned read length default value (60b9230)
Fix extension checking for input files (6c4f91e)
set snakemake keepgoing to True as a default (0076d52)
use the correct columns of input BED file when there are more columns given than necessary (56b5259)
workaround for Argument list too long error when parsing complex workflows (2835c44)

Performance Improvements¶

change make_pickle rule to localrule (f41cc01)
change threads in local execution mode to improve parallel performance (869c81a)

Dependencies¶

add Rich as a dependency with version 13.. (e63cac7)
update AmpliGone to version 1.2.0 (dfb22f1)

Documentation¶

update documentation to include presets functionalities (adc5265)

1.1.0 (2022-12-06)¶

Features¶

add base of functionality to translate and write amino acid sequences (25884b7)
translate and extract aminoacids sequences for multiple targets (657aaff)

Bug Fixes¶

add the missing "FORWARD" and "REVERSE" primer keywords (74b92c6)
change found features to np.nan if input reference and features file don't match (3e812e4)
circumvent issue where null values cause problems in data translation steps (6007fca)
correctly parse amino acids that have a name with a dot in it (3e14dd5)
make sure all required info is present when no gff files are given (d589989)

Documentation¶

clarify some sections in the docs (9bc4171)
fix broken links (9bc4171)
update documentation to match new functionality (9bc4171)

Dependencies¶

add AminoExtract to dependency list (acb378e)
change minimal python version to 3.10 (acb378e)
pin AminoExtract version to v0.2.0 (cce1cf9)
pin AminoExtract version to v0.2.1 (c0e869f)
update TrueConsense to v0.5.0 and change rules accordingly (af15b9c)
update TrueConsense version to 0.5.1 (b1a61e4)

1.0.4 (2022-11-01)¶

Bug Fixes¶

cleanly exit vcf_to_tsv.py script when vcf is empty after filtering (037467b)
replace bcftools with python script to avoid bcftools shared libraries error (eefaead)

Dependencies¶

remove bcftools as a dependency (eefaead)
remove the entire Mutations environment as it is no longer necessary (eefaead)

1.0.3 (2022-10-12)¶

Dependencies¶

pin snakemake to version 7.15.2 for dependency compatibility (0914b56)
set snakemake 7.15.2 as a minimal version in setup.py (0914b56)

1.0.2 (2022-08-15)¶

Dependencies¶

update AmpliGone to version 1.1.0 (153719d)
update included snakemake version to 7.12.x (e59edf9)
use the bioconda channel to install AmpliGone instead of pip (0f1fd65)

1.0.1 (2022-04-26)¶

Bug Fixes¶

correctly exit amplicon_coverage calc when only one side of an amplicon could be found combined with low coverage samples (aa77006)
ensure the split reference sequences are always in uppercase (fcf034c)

1.0.0 (2022-04-14)¶

⚠ 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)

0.4.2 (2022-04-12)¶

Bug Fixes¶

limit the self-updater to only update minor and patch versions (f864f55)

0.4.1 (2022-03-08)¶

Bug Fixes¶

correct the memory assignment and threads for RemovePrimers job when no primers are given (a9ebe02)

0.4.0 (2022-02-04)¶

Features¶

add an adjustable mismatch rate for the primer search (7fc4265)
dynamically set usable cpus/threads in local execution mode (1ec85bb)
Write a short report with the used/configured settings of the analysis (0c46366)

Bug Fixes¶

add missing --skip-updates flag (f360161)
corrected update function parameters (7f37d90)
finish an analysis when empty input fastq files are given (d178587)
properly exit with right exit codes and print closing message (f1bbe13)

Performance Improvements¶

tweak read qc filtering settings (b3aab5a)
use adjusted mm2 mapping settings in nanopore-mode (c027daa)

Dependencies¶

add FPDF version 1.7.2 to dependency lists (cfcd9ee)
add lenient version requirements to mamba (07ebfcc)
add urllib3 v1.26 to dependency list for the auto-updater (cfcd9ee)
change biopython version in python setupfile (07ebfcc)
change pysam to lenient versioning (cfcd9ee)
inlcude conda (lenient) version 4.11.x in main env for compatibility (cfcd9ee)
pin pysamstats version to 1.1.2 (cfcd9ee)
pin tqdm (lenient) version to 4.62.x (cfcd9ee)
pin TrueConsense to version 0.3.0 (cfcd9ee)
remove pysamstats from 'clean' environment (cfcd9ee)
update AmpliGone 0.4.0 → 0.4.1 (ea06728)
update AmpliGone 0.4.1 → 0.4.3 (af62d22)
update AmpliGone version 0.2.3 → 0.4.0 (cfcd9ee)
update bcftools 1.12 → 1.14 (cfcd9ee)
update bedtools 2.29.2 → 2.30.0 (cfcd9ee)
update biopython 1.78 → 1.79 (cfcd9ee)
update fastp 0.20.1 → 0.23.2 (cfcd9ee)
update fastqc 0.11.8 → 0.11.9 (cfcd9ee)
update minimap2 & mappy 2.17 → 2.24 (cfcd9ee)
update multiqc 1.9 → 1.11 (cfcd9ee)
update pandas 1.2.3 → 1.3.5 (cfcd9ee)
update parmap 1.5.2 → 1.5.3 (cfcd9ee)
update PyYaml 5.4.1 → 6.0 (cfcd9ee)
update samtools 1.11 → 1.14 (cfcd9ee)
update seqkit 0.14.0 → 2.1.0 (cfcd9ee)
update snakemake 6.4.1 → 6.13.1 (cfcd9ee)

Documentation¶

add importance of primer name and number to docs (7107398)
include primer mismatch rate flag to documentation (531f526)
update installation instructions (5944d22)

0.3.0 (2021-11-15)¶

Features¶

allow ViroConstrictor to update itself to latest release (11ad616)
flexible memory requirements per workflow job (7c189cd)

Bug Fixes¶

change consensus calling to a 'mid' cpu-task (3094b78)

0.2.3 (2021-11-03)¶

Documentation¶

add explanatory comments to docs config (f3e05ec)

0.2.2 (2021-11-03)¶

Bug Fixes¶

change amplicon covs script to complete with empty input #5 (6900638)
complete workflow with primers set to NONE (47becf8)
use 'map-ont' mm2 preset in nanopore workflow (f89d5cf)