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sanger-tol
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genomenote
This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.
https://pipelines.tol.sanger.ac.uk/genomenote
MIT License
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Resource optimisation
#92
muffato
closed
10 months ago
3
Leftover files in /tmp from the `sort` commands
#91
muffato
closed
9 months ago
0
Resource optimisation
#90
muffato
closed
10 months ago
1
Deprecate generating the `.genome` file
#89
muffato
closed
10 months ago
2
Order the contact map like the karyotype
#88
muffato
closed
5 months ago
0
ERROR ~ toIndex = 2 -- Check script 'genomenote/./workflows/genomenote.nf' at line: 98
#87
mdozmorov
opened
11 months ago
4
Update maxRetries
#86
priyanka-surana
closed
11 months ago
3
Changes to fix failing tests. Refactored parsing of metadata files to…
#85
BethYates
closed
11 months ago
2
Check that the JSON coming from `datasets` contains an assembly
#84
muffato
closed
11 months ago
2
Get the BUSCO ODB name from the BUSCO definition file rather than GoaT
#83
muffato
closed
11 months ago
2
Configure structure of HiGlass ingress directory
#82
BethYates
closed
11 months ago
3
#78 review - as commits
#81
muffato
closed
1 year ago
1
Inconsistent variable names in the DOCX template
#80
muffato
closed
3 months ago
0
meta.id confusion
#79
muffato
opened
1 year ago
0
Update higlass
#78
BethYates
closed
1 year ago
6
Reinstate CI on GitHub
#77
muffato
closed
1 year ago
3
updated ncbi container
#76
priyanka-surana
closed
1 year ago
3
Genome metadata
#75
BethYates
closed
1 year ago
1
Added the CI workflows to test the pipeline on the Sanger farm via Tower
#74
muffato
closed
1 year ago
3
Optional readmapping subworkflow
#72
priyanka-surana
opened
1 year ago
0
Genome metadata
#71
priyanka-surana
closed
5 months ago
0
Genome metadata added module to produce a docx file from a genome note template file and genome metadata parameter file
#70
BethYates
closed
1 year ago
4
Genome metadata
#69
BethYates
closed
1 year ago
1
Public dev merged
#68
BethYates
closed
1 year ago
3
Merging main into dev
#67
priyanka-surana
closed
1 year ago
1
disable ci
#66
priyanka-surana
closed
1 year ago
1
Genome metadata
#65
BethYates
closed
1 year ago
1
For release
#64
priyanka-surana
closed
1 year ago
1
Template update
#63
priyanka-surana
closed
1 year ago
12
Cooler dump
#62
priyanka-surana
closed
1 year ago
0
Genome metadata
#61
BethYates
closed
1 year ago
3
Genome metadata
#60
BethYates
closed
1 year ago
2
Make chromosomes optional #58
#59
priyanka-surana
closed
1 year ago
0
Make chromosomes optional
#58
priyanka-surana
closed
1 year ago
0
Fastk
#57
priyanka-surana
closed
1 year ago
1
Update create table
#56
priyanka-surana
closed
1 year ago
1
Add support for multiple PacBio kmer databases
#55
priyanka-surana
closed
1 year ago
1
FastK optional module
#54
priyanka-surana
closed
1 year ago
0
Get HiC Mapping result in summary table
#53
priyanka-surana
closed
1 year ago
0
Headers created without content
#52
priyanka-surana
closed
1 year ago
0
Remove `bedtools_sort`
#51
priyanka-surana
closed
1 year ago
0
Update `create_table` to deal with optional inputs
#50
priyanka-surana
closed
1 year ago
0
N50 from GoaT not always available
#49
priyanka-surana
closed
1 year ago
2
update `bedtools_bamtobed` config settings
#48
priyanka-surana
closed
1 year ago
0
Update bed_filter
#47
priyanka-surana
closed
1 year ago
1
update dev
#46
priyanka-surana
closed
1 year ago
7
Unnecessary sort
#45
muffato
closed
1 year ago
0
Merqury
#44
priyanka-surana
closed
1 year ago
6
Busco
#43
priyanka-surana
closed
2 years ago
1
N50
#42
priyanka-surana
closed
2 years ago
0
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