phylociraptor v0.9.5

Changes since last release:
075856a Update to automated release action
a8b665d Create github action workflow for automated release
648ae43 report: Further improvements for --figure mode. Version push to 0.9.5
5ee8dae report: Several more small improvements for --figure
9ebd7d0 report: Several small improvements for the --figure mode.
d51acd2 phylociraptor: remove git remnents after merge conflict
1a24f00 Add phylocriptor script again after conflict
fff2464 report: Add experimental feature to create a condensed report figure
e5cd5a9 phylociraptor-docker: Fix problem in Dockerfile. bc is now installed before users are created
b9367fc modeltest: change standard behavior of iqtree gene trees so that failed analyses can be continued by default.
bcfbcbe orthology: It is now easier to handle datasets consisting of genomes and transcriptomes. increase version to 0.9.4
0eadf43 phylociraptor-docker: add bc command installation to Dockerfile
78db5c5 report: Make sure report can also be created in phylociraptor-docker
65e8792 phylociraptor: fix small bug in orthology determine submission mode
412f40d phylociraptor: make --rerun-incomplete an option that can be passed directly to snakemake from the phylociraptor script
506db30 report: cosmetics
05012e2 report: Cosmetics. Display version in report. Display no. of alignments for full, trimmed and filtered alignments
62be00e report: Fix incorrect reporting of busco set name and number of busco genes. Display none when failed_genes is empty
aa9ed0b report: Fix error in modeltest and genetree reporting when only a single parameter combination is used
9211ea1 version push to 0.9.3
bd406d1 report: cosmetics of tables
d56a378 report: Add reporting of final trees as a table
2ca2116 Code cleanup: Remove obsolete yaml env files
2571566 docs: Add minimal example tutorial to docs
6a6c0eb test-cases: Small update to README of minimal testcase
c38e83f test-cases: After more info to readme of minimal testcase, plus changes after successful runthrough
904a9bf Add minimal testcase
ea1911e phylociraptor: Move version to external file and make sure phylociraptor-docker tags the correct version automatically
4e08d82 docs: add several explanations about known problems and add some text for the indepth part
7db8c00 mltree: fix problem with error in iqtree partition nexus file
d23f02e setup: make sure genome download checkpoint folder is created before touching the checkpoint file.
b8bf274 Update README file
e791b43 phylociraptor: Display versions also in different modules
29268df report: Make genetree violin plots interactive. Rename some of the tabs. Add correct parsimony cutoffs to trimmed and filtered alignments
ca5fe2a modeltest: Fix bug path in how mean bootstrap is calculated. Now the correct folder is specified
2c8a0e9 phylociraptor: Fix parsing of singularity arguments. Version push to 0.9.2
edeb9e8 It is now possible to impose one or several bootstrap cutoff values to select the genes used for tree calculation. This is done by evaluation the mean bootstrap values of each gene tree. Gene trees are now estimated incl. bootstrap analysis during the modeltest step
a505d03 modeltest: Rename model to modeltest
e113704 model: Full gene trees are now calculated during this step incl. full boostrap analysis. Mean bootstrap values are also saved at the end of this step for subsequent tree steps. This saves time and reduces the number of jobs
936da37 mltree, njtree: Possibility to filter genes based on bootstrap cutoff
c0647a2 Another fix for Docker phylociraptor file permissions
c03fe77 Add Conditional to make Docker Container work the same on Linux and Mac
f20d919 fix problems with files permissions when phylociraptor is run with Docker on Linux
2b0501c Add possibility to run phylociraptor completely inside a Docker container
fdf3446 test-cases: Fix errors in config.yaml for fungal testset
5f9762e setup: fix error in busco set download rule
22620ac speciestree: It is now possible to filter species trees based on their average bootstrap support. This can be set in the config.yaml file. The report also displays this now. Version push to 0.9.1
df279f8 test-cases: Fix arthropoda busco set link
ef76a57 Update Readme
d03a9f8 Add files for test case arthropoda. Remove email from config.yaml in the fungi testcase
c332595 Add files for test case fungi
7fd9217 tar software outputs from busco in single archive
748e794 setup: download busco set: fix problem where certificates have changed when downloading the BUSCO set.
999f9d7 mltree: fix wrong reference to raxml config file entry
359ab83 phylciraptor: small change to three part version number
14a8456 report: add additional output to final alignment filtering and trimming rule for use with the report. Update report to include and use all the information from alignment, trimming and filtering.
cea10db phylociraptor: Report version auf dependencies in every runmode
5f0cd13 phylociraptor: Report sankemake and singularity version when --debug is enabled
9b7fb68 phylociraptor: report version and git commit correctly. Enable -v flag which did not work previously
64faa56 phylociraptor: Additional modifications and better output labeling
52994f6 phylociraptor: Now it is possible to provide additional arguments for snakemake and singularity. Add timestamp to output. Code cleanup.
91fb73d doc: Several updates to documentation to account for some of the new features
d4d0cab speciestree: Change iqtree behavior to always use the number of specified threads without -nt AUTO and -ntmax
5b13e49 setup: Make sure output files are created correctly when there are no genomes to download
001b6aa report: Use different palette in case there are more than 11 colors for modeltest to display.
78faab3 Another fix for README
0d445e8 Update README
96a4784 phylociraptor: Add nerdy ASCII font
682b49e cleanup run_busco, fix logging issues
0726929 cosmetic - add batch number to download message
7d02c31 allow to choose between 2 BUSCO versions
d755fba cosmetic change - remove verbose and fix warning
3ab51f1 filter-align: Modify filter-align to use now concurrency location, add missing rules to cluster config files
dd47e07 mltree: enable passing on additional_params to iqtree and raxml
4c2107f Remove several unused scripts from the early days of the pipeline
b57d822 phylociraptor: Make sure dependency list is passed correctly (under quotes) to immediate-submit on SGE
3c82224 immediate-submit: Update submodule to latest commit
a95a8d4 align: Change location of concurrency setting in yaml file. Add missing rules to cluster config files
3f8effb filter-orthology: Correctly create statistics file. Move concurrency setting to global setting in config file
b1256ee some cosmetic in setup rule
0f31ddc rename faild report so it matches with rule expectations
966f567 add failed file as ouptut in download_genomes rule
c768d88 setup: Parallelize genome download.
989c58f report: Add common legend for plots in modeltest section
b1a67af docs: Several updates to documentation - change tree to ml tree, add info in some runmodes
9a9adbf phylociraptor check: change how mltree output is determined, there are multiple possible folder combinations
19522ca report: Change how BUSCO results are displayed. Now as a table, before as PNG
d4a7441 orthology, filter-orthology: Fix problem with location of benchmark files which messes up report
1f563d9 Change tree runmode name in README
cf95325 Remove rulegraph files
db88bed phylocirpator: change name of tree mode to mltree. Add --debug flag. Modify check so that it handles multiple combinations of aligners and trimmers at different steps. Change paths to output files and directories to match new directory structure
6897ed3 speciestree: Change location of required input files to new structure
2d88bdc tree: Change location of required input files to new structure
ee6adb3 model: change output file locations so they match new directory structure
6b80339 concatenate: Change input file locations to match new folder structure
ee5dad4 filter-align: Change output file locations and locations of checkpoints so that the match new naming scheme
9625908 align: Determine concurrency limit. Fix output check files for align rules
6528453 filter-orthology: Determine limit for concurrency, change paths to match updated paths in orthology.
c6b93f7 orthology: Additional fixes to busco result locations
b90ad30 Update location of output files to new folder structure
5983f6a Comment out unnecessary prepare augustus rule
4c00494 Change location of mode output files to results/checkpoints/modes. Move unused Snakefile tp rules/
fe63fa1 First set of changes to display results from multiple aligner/trimmer combinations
819b3a3 Fix small problem with statistics files in filter_alignments rule
0bea649 Change location of trimming and filtering statistics to make them easier to parse in R
7ede343 Fix formatting of overview alignment statistics files
25d7621 Change location and naming of alignmint statistics files for report. Reformat output of overview alignment statistics so it is easier to parse.
1242ce7 Change location of busco_set to results/orthology/busco/busco_set
8375622 change file rulename in orthology
aabf048 update config.yaml.template and TODO
0cfd1a7 add thread control to serial mode
b65f541 adjust checkpoint file names after unifying them in the snakefiles
b75db17 adjust structure and paths (tree related) to allow parallel aligners/trimming
0fea347 adjust structure and paths to allow parallel aligners/trimming
5b80193 enable two alignment trimmer in parallel for results from multiple aligners
bee6a8f enable two aligners in parallel
c4f466f update results structure (filter-orthology)
ae97733 add information on species tree and njtree modes to indepth
a429e55 update documentation
c838d14 add thread to mafft and missing rules to SLURM template
0a16959 fix logging issue
2e137d0 handle create_sequence_files in batches
0dc0801 add exclude functionality to orthology part
bf45ca1 add specific...

backup_old_version

This release is merely to backup the "old" phylociraptor before large parts have been rewritten and improved.