CHANGELOG.md 2.31 KB
Newer Older
peguerin's avatar
peguerin committed
1
2
3
# Changelog
All notable changes to this project will be documented in this file.

peguerin's avatar
peguerin committed
4
5
6
7
8
9
10
11
12
13
14
## [unreleased] - 9th february 2020
### Added

* copy and rename files generated from results/18_table_assigned_sequences/ to results/ folder
* `script/cat_samples_into_runs.sh` bash script to merge {sample} files into {projmarkrun} file

### Changed

* all worklows are merged into a single one
* results subfolders are generated automatically
* unique scripts, rules and envs folders
15
* Fix SettingWithCopyWarning pandas dataframe
peguerin's avatar
peguerin committed
16
17
18
19
20
21
22
23
24

### Removed

* old folders and scripts 01_settings, 02_assembly, 03_demultiplex, etc...
* old preexisting subfolders into results folder
* clean.sh script which is now useless
* rename.sh script which is replaced by a rule in Snakefile


peguerin's avatar
peguerin committed
25
## [1.1.4] - 16th september 2020
peguerin's avatar
peguerin committed
26
27
### Added

peguerin's avatar
peguerin committed
28
29
30
* can handle 2 different types of input format CLASSIC and RAPIDRUN
* tutorial to process data in CLASSIC format based on a subset of Rhone project data

peguerin's avatar
peguerin committed
31
32
33
34
35
36
37
38
39
### Changed

* rapidrun all_samples.tsv replaced by all_samples.csv with `;` as separator

### Removed

* Unuseful or deprecated config files


peguerin's avatar
peguerin committed
40
## [1.1.3] - 27th july 2020
peguerin's avatar
peguerin committed
41
42

### Added
peguerin's avatar
peguerin committed
43

peguerin's avatar
peguerin committed
44
* tutorial commands and folders
peguerin's avatar
peguerin committed
45
* tutorial configuration file
peguerin's avatar
peguerin committed
46
* clean.sh a script to remove intermediate files, log files and final results files
peguerin's avatar
peguerin committed
47

peguerin's avatar
peguerin committed
48
49
50
51
52
53
54
### Changed

* main.sh launches whole workflow
* fix tutorial commands


## [1.1.2] - 21st july 2020
peguerin's avatar
peguerin committed
55
56
57
58
59
60
61
62
63

### Added

* multithreaded assembly step for large fastq files

### Changed

* fix main.sh so it can run into a single command

peguerin's avatar
peguerin committed
64
65
66
67
### Removed

* picture of DAG files

peguerin's avatar
peguerin committed
68

peguerin's avatar
peguerin committed
69
## [1.1.1] - 3rd july 2020
peguerin's avatar
peguerin committed
70

peguerin's avatar
peguerin committed
71
72
73
### Added

* Tutorial
peguerin's avatar
peguerin committed
74
* Documentation
peguerin's avatar
peguerin committed
75
* gitignore
peguerin's avatar
peguerin committed
76
77
78
* Autorship
* license MIT
* Singularity/Docker recipe for obitools
peguerin's avatar
peguerin committed
79

peguerin's avatar
peguerin committed
80
## [1.1.0] - 22th june 2020
peguerin's avatar
peguerin committed
81
82
83
84

### Added

* data test
peguerin's avatar
peguerin committed
85
86
87
88
89
90
91
* Conda v4.8.2 envs

### Changed

* upgrade snakemake to v5.19.2
* new structure for distribution based on snakemake recommandation [here](https://snakemake.readthedocs.io/en/v5.19.2/snakefiles/deployment.html)

peguerin's avatar
peguerin committed
92
93
94
95
96
### Removed

* infos folder


peguerin's avatar
peguerin committed
97
98
99
## [1.0.1] - 14th june 2020

### Changed
peguerin's avatar
peguerin committed
100
101
102
103

* Absolute path of all_samples.tsv into config.yaml
* Remove redundant paramters into config.yaml
* Fix name of count parameters into filter_samples.smk
peguerin's avatar
peguerin committed
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119


## [1.0.0] - 25th may 2020

### Added
 
* Complete workflow
* snakemake rule system to handle rapidrun files

### Changed

* upgrade singularity to v3.6

### Removed

* marker.csv