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sanger-tol
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genomenote
Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.
https://pipelines.tol.sanger.ac.uk/genomenote
MIT License
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Support Hi-C files in BAM format
#102
muffato
closed
11 months ago
4
Create link to map on higlass server and don't duplicate files on higlass server
#101
BethYates
closed
9 months ago
12
Agree on which Busco lineage to use for which species
#100
muffato
opened
11 months ago
0
Busco, FastK on large genomes, Completeness
#99
muffato
closed
11 months ago
3
Populates latest Genome Notes template with information from both the GENOME_METADATA subworkflow and the GENOME_STATISTICS subworkflow
#98
BethYates
closed
11 months ago
3
Need to factor the attempt number in as well
#97
muffato
closed
12 months ago
1
bugfix: Need to use collect() to make it a list
#96
muffato
closed
12 months ago
1
Documentation updates for the release
#95
muffato
closed
11 months ago
2
1.1 release
#94
muffato
closed
10 months ago
8
Hotfixes for production
#93
muffato
closed
1 year ago
6
Resource optimisation
#92
muffato
closed
1 year ago
3
Leftover files in /tmp from the `sort` commands
#91
muffato
closed
11 months ago
0
Resource optimisation
#90
muffato
closed
1 year ago
1
Deprecate generating the `.genome` file
#89
muffato
closed
1 year ago
2
Order the contact map like the karyotype
#88
muffato
closed
6 months ago
0
ERROR ~ toIndex = 2 -- Check script 'genomenote/./workflows/genomenote.nf' at line: 98
#87
mdozmorov
closed
1 month ago
4
Update maxRetries
#86
priyanka-surana
closed
1 year ago
3
Changes to fix failing tests. Refactored parsing of metadata files to…
#85
BethYates
closed
1 year ago
2
Check that the JSON coming from `datasets` contains an assembly
#84
muffato
closed
1 year ago
2
Get the BUSCO ODB name from the BUSCO definition file rather than GoaT
#83
muffato
closed
1 year ago
2
Configure structure of HiGlass ingress directory
#82
BethYates
closed
1 year ago
3
#78 review - as commits
#81
muffato
closed
1 year ago
1
Inconsistent variable names in the DOCX template
#80
muffato
closed
5 months ago
0
meta.id confusion
#79
muffato
closed
1 month 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
7 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
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