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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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Release 2.1.0
#152
BethYates
opened
3 days ago
1
Add ensembl metadata check
#151
BethYates
closed
3 days ago
2
Added annotation statistics subworkflow
#150
BethYates
closed
3 days ago
1
Ci compute update
#149
gq1
closed
1 month ago
6
Allow inclusion of multiple species in a single genome note
#148
BethYates
opened
1 month ago
1
Update CITATION.cff
#147
tkchafin
closed
1 month ago
1
Release 2.0.0
#146
BethYates
closed
1 month ago
1
Release 2.0
#145
BethYates
closed
1 month ago
1
Release 2.0 fixes
#144
BethYates
closed
1 month ago
5
Merge changes on dev into public_dev ahead of preparation for release 2.0
#143
BethYates
closed
1 month ago
2
Added Busco to run in protein mode
#142
SandraBabirye
closed
3 weeks ago
4
Add BUSCO to the annotation_statistics subworkflow
#141
BethYates
closed
4 days ago
2
Added GBIF as a metadata source
#140
SandraBabirye
closed
1 month ago
6
Switch back to `scratch=false` for large genomes
#139
muffato
closed
2 months ago
1
updated to main from master
#138
BethYates
closed
2 months ago
2
Added a new feature branch 'copo_metadata' to solve issue #115
#137
SandraBabirye
closed
2 months ago
1
Added new local module to extract only relevant annotation statistics
#136
SandraBabirye
closed
2 months ago
2
Added new subworkflow 'ANNOTATION_STATS' and new parameter --annotation_set to solve issue #121
#135
SandraBabirye
closed
3 months ago
2
Added new subworkflow "ANNOTATION_STATS" and parameter --annotation_set to solve issue #121
#134
SandraBabirye
closed
3 months ago
1
Added a new subworkflow to solve issue #121 to calculate the summary statistics from an annotation file
#133
SandraBabirye
closed
3 months ago
1
Allow running of metatdata subworkflow on different biosample types
#132
reichan1998
closed
3 months ago
1
added a sub workflow to solve issue #121 in order to obtain the gene statistics from an annotation file (gff3)
#131
SandraBabirye
closed
3 months ago
2
Added subworkflow to solve #121 issue for genome note pipeline
#130
SandraBabirye
closed
3 months ago
1
Added a new sub workflow #annotation_statistics.nf that outputs the annotation statistics in the gff3 file to solve issue #121
#129
SandraBabirye
closed
3 months ago
1
Added a new branch to solve the #121 issue on the genome note pipeline
#128
SandraBabirye
closed
4 months ago
0
Patch 1.2.1: Fix issue where pipeline fails on missing fields from NCBI datasets JSON
#127
tkchafin
closed
3 months ago
4
ERROR pipeline failure when fields missing from NCBI genome report [v1.2.0]
#126
tkchafin
closed
3 months ago
0
Add GBIF to the metadata sources
#125
BethYates
closed
1 month ago
1
MUMmer
#124
BethYates
opened
5 months ago
0
GenomeScope
#123
BethYates
opened
5 months ago
0
Flagger
#122
BethYates
opened
5 months ago
0
Sub-workflow for gene statistics
#121
BethYates
opened
5 months ago
3
Make BUSCO annotations an optional input
#120
muffato
opened
5 months ago
1
Refine input params
#119
BethYates
closed
1 month ago
0
Set Higlass config default values
#118
BethYates
closed
1 month ago
0
Merqury and Meryl
#117
BethYates
opened
5 months ago
0
Add GFA stats
#116
BethYates
opened
5 months ago
0
Add COPO to the metadata sources
#115
BethYates
closed
1 month ago
1
Allow running of metatdata subworkflow on multiple specimen IDs
#114
BethYates
closed
3 months ago
2
Ci resource increase
#113
gq1
closed
6 months ago
3
1.2 release
#112
muffato
closed
6 months ago
3
Bugfix: the BAM still needs to be filtered with `-F0x400`
#111
muffato
closed
6 months ago
1
Allow population of either an XML or docx genome note template
#110
BethYates
closed
8 months ago
3
Error executing process GENOME_STATISTICS:SUMMARYSEQUENCE with invalid assembly accession
#109
mtammami
closed
1 month ago
2
Stopped forcing eutheria_odb10
#108
muffato
closed
9 months ago
2
Updated test species and test data for small test.
#107
BethYates
closed
10 months ago
1
Set use_work_dir_as_temp to true when running at the Sanger
#106
muffato
closed
10 months ago
4
Misc changes for running the pipeline on the Danioninae species
#105
muffato
closed
11 months ago
2
Report all samples in the statistics CSV
#104
muffato
closed
6 months ago
0
Allow generating contact maps for multiple samples
#103
muffato
closed
6 months ago
3
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