-
Notifications
You must be signed in to change notification settings - Fork 2
/
changelog.txt
122 lines (94 loc) 路 5.52 KB
/
changelog.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
2.7.2
- Compressed test files.
- Updated header text
- Add --no-check-certificate to wget downloads.
2.7.1
- Breaking change: File hierarchy now follows what is recommended in the snakemake documentation. Rules are now in individual files.
- Breaking change: profiles/ moved to profile/ (sorry). And local profiles are now named "default".
- Busco runs in protein mode, reusing .faa from prokka (or bakta - see further down). Should result in speedup.
- Added Panaroo, removed Roary.
- For dbcan, only the substrates are shown in the dynamic report.
- Gtdb updated to release 220.0
- Add bakta.
- User can specify whether to use prokka or bakta to create annotation that is used for dbcan, interproscan diamond_kegg, busco. This can be set using `--config annotator=bakta` or by changing the permanent parameter in config/config.yaml.
- Add eggnog
- rename benchmark files from individual->Sample
- Add antismash. Uses .gbk from prokka.
- report_subpipeline renamed to dynamic_report
- Dynamic report is now run by the ./asscom2 binary instead of using onsuccess/onerror.
- Minor fixes.
- Software versions and database versions are written to hidden files within output directories.
- Added dynamic parameters to prokka and iqtree to the config file.
- Added support for a "fofn" which is a file of file names. In the tseemann style, it defines which input genomes to process.
- Use KEGG KO from eggnog in kegg_pathway. If this doesn't work well I'll consider re-implementing kofam_scan which was removed long time back. Now a_class and b_class are "class" and "group".
- Implemented a way to set the output directory which now defaults to the old static "results_ac2".
- Implemented TreeCluster that on the 4.5% and 10% basis defines clusters on the mashtree distances so the user can easily get an impression on the relative differences between samples.
- Fix an error that makes snp-dists results not show up in the report. (Thanks to @AstaLaugesen)
- Added documentation over at https://assemblycomparator2.readthedocs.io/en/latest/
2.6.2
- Fix wrong path for dbcan results (not yet implemented in report)
- Downgrade diamond 2.1.8 due to segfault in newest version (2.1.9) https://github.com/bbuchfink/diamond/issues/785
2.6.1
- Remove Kraken2, hence new minor version. Kraken2 really only makes sense on reads.
- Roary as a checkpoint, to only continue with iqtree, fasttree and snp-dists if the core genome is non-empty.
- conda yaml for wget. TODO, carry over to dbcan download as well.
2.5.18
- Support for weird characters in input files. #31
- Support for adding input files from other directories. #58
- Minor bugfixes. #77
- Test battery is being developed. (https://github.com/cmkobel/ac2-test-battery)
2.5.17
- Forced recompilation of docker image did not fix issue #74. This patch has equivalent .yaml-files to version 2.5.14, which means that the old (working) docker image will be compatible.
2.5.16
- Indirect bug because of an uncaught docker error. Forced recompilation of the image should fix that.
- Propagation of version string to easy version bumping.
2.5.15
- Limited snakemake version because of breaking dependency changes herein.
2.5.14
- problems with dockerfile fixed
2.5.13
- Bugfix: Wrong number of bootstraps for quicktree
2.5.12
- motulizer.yaml was missing.
2.5.11
- Added support for motulizer and motupan. Yet lacking in report and awaits further integration.
2.5.10
- assemblycomparator2 now supports iqtree with bootstrapping. Runs on the core genome produced by roary. Yet to be included in the report.
2.5.9
- Fixed an error where checkm2 would fail setting the download location internally when running asscom2 using the apptainer/docker container. https://github.com/chklovski/CheckM2/issues/73
2.5.8
- Fixed an error where a different version of the docker image would be pulled for the report subpipeline
2.5.7
- Fixed an error where a conda environment would not be activated when using the apptainer profile for slurm.
2.5.6
- New ./asscom2 "binary" to replace the old alias. This "binary" comes with default environment variables.
2.5.5
- Use $ASSCOM_DATABASES to define where the databases are placed.
- Docker images have a versioning system so an incompatible image can't be used.
2.5.4
- Using the mashtree order in plots in the report. Using alphabetical order redundantly in case mashtree hasn't run (sucessfully). Minor adjustments to other plots. TODO: midpoint root tree somehow and order all tables in the report as well.
2.5.3
- Using snakemake's --containerize to automatically generate images which are then synced to dockerhub as cmkobel/assemblycomparator2. Support for hpc queues isn't yet tested.
2.5.2
- dbcan, including download
- interproscan
- both dbcan and interproscan are yet to be integrated in the report
2.5.0
- Apptainer support. New profiles for apptainer or conda use.
2.4.1
- Adjusting the new report and fix minor bugs
2.4.0
- New report based on child sections
2.3.0
- Disabled pathway enrichment as conda failed
- Implemented GTDB-tk
- Having problems with Prokka
2.2.0
- Sample pathway enrichment analysis with clusterProfiler which is integrated into the report.
- Considering going away from singularity: Too much maintenance and too little return when it has to work with conda anyway. I haven't completely decided yet, but leaning strongly.
2.1.1
- Simple GC statistics added to output and report
2.1.0
- Bug and stability issues fixed
2.0.0
- Completely new system based on snakemake using both slurm and singularity