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elsasserlab
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minute
MINUTE-ChIP data analysis workflow
https://minute.readthedocs.io
MIT License
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Optimize minute environment setup
#190
cnluzon
opened
2 months ago
3
More customized alignment to reference including strobealign
#189
cnluzon
opened
4 months ago
0
Bowtie2 configurable alignment mode
#188
cnluzon
closed
4 months ago
1
Rename percentage duplication field
#187
cnluzon
opened
5 months ago
0
Produce only bigWig for pools of replicates
#186
cnluzon
closed
6 months ago
0
Move all testdata to GitHub
#185
cnluzon
closed
6 months ago
3
minute run initialization improvements
#184
cnluzon
closed
6 months ago
1
Link to GitHub repository in docs TOC
#183
marcelm
closed
6 months ago
2
Cleanup minute documentation
#182
cnluzon
closed
6 months ago
0
Fix MultiQC output file name
#181
marcelm
closed
6 months ago
6
Bump micromamba version
#180
marcelm
closed
6 months ago
2
No longer recommend using Mamba
#179
marcelm
closed
6 months ago
4
pytz dependency not met in recent builds of conda environment
#178
cnluzon
closed
6 months ago
4
Adjust INRC barplots size for large runs
#177
cnluzon
opened
7 months ago
0
bowtie2 2.5.2 crashes when skipping some reads due to read length
#176
cnluzon
opened
10 months ago
2
QC report improvements
#175
cnluzon
closed
10 months ago
1
MkDocs documentation
#174
cnluzon
closed
11 months ago
1
Mapping quality parameter
#173
cnluzon
closed
11 months ago
2
Read the docs site for minute
#172
cnluzon
closed
11 months ago
1
Better handling of minute init --input parameter
#171
cnluzon
closed
1 year ago
1
Set up the Conda environment with setup-micromamba
#170
marcelm
closed
1 year ago
2
Modernize project layout
#169
marcelm
closed
1 year ago
2
minute init with a simplified barcodes.tsv specification
#168
cnluzon
closed
1 year ago
1
INRC barplots y-axis fix
#167
cnluzon
closed
1 year ago
0
Reinstate quick as a synonym of default run
#166
cnluzon
closed
1 year ago
2
Add a rule to run minute without generating bigwig files
#165
cnluzon
closed
1 year ago
0
Generate missing bowtie2 index files
#164
cnluzon
opened
1 year ago
3
Remove dynamic rule naming
#163
cnluzon
closed
1 year ago
1
Make minute generate bowtie2 index if no index is found
#162
cnluzon
opened
1 year ago
0
Fragment length parameter not so necessary for bigWig generation
#161
cnluzon
opened
1 year ago
0
MultiQC reporting updates
#160
cnluzon
closed
1 year ago
3
snakemake >= 7.18.2 crashes renaming anonymous rules in some cases
#159
cnluzon
closed
1 year ago
3
New custom deduplication method based on UMI-tools API
#158
cnluzon
closed
2 years ago
4
command line cheat sheet
#157
simonelsasser
closed
1 year ago
2
BAM file remove unmapped reads
#156
simonelsasser
opened
2 years ago
0
wrapped snakemake run on cluster mode inherits max ncores from scheduler process
#155
cnluzon
opened
2 years ago
0
Print nicer error message for incorrect number of fields in TSV
#154
marcelm
closed
2 years ago
0
Spaces in group name in groups.tsv break the run
#153
cnluzon
closed
2 years ago
2
Add MIT license
#152
marcelm
closed
2 years ago
0
Set version number in setup.cfg
#151
marcelm
closed
2 years ago
0
Rename config.yaml to minute.yaml
#150
marcelm
closed
2 years ago
0
MultiQC custom data reports fix
#149
cnluzon
closed
2 years ago
4
Add "minute init" subcommand
#148
marcelm
closed
2 years ago
6
Rename config.yaml to minute.yaml
#147
marcelm
closed
2 years ago
0
Generated scaling stats missing from the MultiQC report
#146
cnluzon
closed
2 years ago
3
Add number of demultiplexed reads to stats summary
#145
cnluzon
closed
1 year ago
1
Add samtools stats to final report
#144
cnluzon
closed
2 years ago
1
Extend reads in unscaled bigwig files
#143
cnluzon
closed
2 years ago
1
Add barcode to read header when demultiplexing
#142
marcelm
closed
2 years ago
1
Include read demultiplexing barcode in the demultiplexed FASTQ read ID
#141
cnluzon
closed
2 years ago
1
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