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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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Add GBIF to the metadata sources
#125
BethYates
opened
2 days ago
0
MUMmer
#124
BethYates
opened
6 days ago
0
GenomeScope
#123
BethYates
opened
6 days ago
0
Flagger
#122
BethYates
opened
6 days ago
0
Sub-workflow for gene statistics
#121
BethYates
opened
6 days ago
2
Make BUSCO annotations an optional input
#120
muffato
opened
1 week ago
0
Refine input params
#119
BethYates
opened
1 week ago
0
Set Higlass config default values
#118
BethYates
opened
1 week ago
0
Merqury and Meryl
#117
BethYates
opened
1 week ago
0
Add GFA stats
#116
BethYates
opened
1 week ago
0
Add COPO to the metadata sources
#115
BethYates
opened
1 week ago
0
Allow running of metatdata subworkflow on multiple specimen IDs
#114
BethYates
opened
1 week ago
0
Ci resource increase
#113
gq1
closed
1 month ago
3
1.2 release
#112
muffato
closed
1 month ago
3
Bugfix: the BAM still needs to be filtered with `-F0x400`
#111
muffato
closed
1 month ago
1
Allow population of either an XML or docx genome note template
#110
BethYates
closed
3 months ago
3
Error executing process GENOME_STATISTICS:SUMMARYSEQUENCE with invalid assembly accession
#109
mtammami
opened
3 months ago
1
Stopped forcing eutheria_odb10
#108
muffato
closed
4 months ago
2
Updated test species and test data for small test.
#107
BethYates
closed
5 months ago
1
Set use_work_dir_as_temp to true when running at the Sanger
#106
muffato
closed
5 months ago
4
Misc changes for running the pipeline on the Danioninae species
#105
muffato
closed
6 months ago
2
Report all samples in the statistics CSV
#104
muffato
closed
1 month ago
0
Allow generating contact maps for multiple samples
#103
muffato
closed
1 month ago
3
Support Hi-C files in BAM format
#102
muffato
closed
6 months ago
4
Create link to map on higlass server and don't duplicate files on higlass server
#101
BethYates
closed
4 months ago
12
Agree on which Busco lineage to use for which species
#100
muffato
opened
6 months ago
0
Busco, FastK on large genomes, Completeness
#99
muffato
closed
6 months ago
3
Populates latest Genome Notes template with information from both the GENOME_METADATA subworkflow and the GENOME_STATISTICS subworkflow
#98
BethYates
closed
6 months ago
3
Need to factor the attempt number in as well
#97
muffato
closed
7 months ago
1
bugfix: Need to use collect() to make it a list
#96
muffato
closed
7 months ago
1
Documentation updates for the release
#95
muffato
closed
6 months ago
2
1.1 release
#94
muffato
closed
5 months ago
8
Hotfixes for production
#93
muffato
closed
7 months ago
6
Resource optimisation
#92
muffato
closed
7 months ago
3
Leftover files in /tmp from the `sort` commands
#91
muffato
closed
6 months ago
0
Resource optimisation
#90
muffato
closed
7 months ago
1
Deprecate generating the `.genome` file
#89
muffato
closed
7 months ago
2
Order the contact map like the karyotype
#88
muffato
closed
1 month ago
0
ERROR ~ toIndex = 2 -- Check script 'genomenote/./workflows/genomenote.nf' at line: 98
#87
mdozmorov
opened
8 months ago
4
Update maxRetries
#86
priyanka-surana
closed
8 months ago
3
Changes to fix failing tests. Refactored parsing of metadata files to…
#85
BethYates
closed
8 months ago
2
Check that the JSON coming from `datasets` contains an assembly
#84
muffato
closed
8 months ago
2
Get the BUSCO ODB name from the BUSCO definition file rather than GoaT
#83
muffato
closed
8 months ago
2
Configure structure of HiGlass ingress directory
#82
BethYates
closed
8 months ago
3
#78 review - as commits
#81
muffato
closed
10 months ago
1
Inconsistent variable names in the DOCX template
#80
muffato
closed
1 week ago
0
meta.id confusion
#79
muffato
opened
10 months ago
0
Update higlass
#78
BethYates
closed
9 months ago
6
Reinstate CI on GitHub
#77
muffato
closed
10 months ago
3
updated ncbi container
#76
priyanka-surana
closed
10 months ago
3
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