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bokulich-lab
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q2-fondue
Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere
BSD 3-Clause "New" or "Revised" License
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Fondue outputs cause errors when running metadata tabulate
#119
lina-kim
closed
2 years ago
2
Scrape hyphenated ID sets in `scrape-collection`
#118
adamovanja
closed
2 years ago
0
Fetch data by experiment and sample IDs
#117
adamovanja
closed
2 years ago
0
ENH: Add scraping of other IDs
#116
adamovanja
closed
2 years ago
3
FIX: Safe library info import
#115
adamovanja
closed
2 years ago
1
ENH: Fetch metadata & sequences by StudyID
#114
adamovanja
closed
2 years ago
1
ENH: Scraping DOI from library
#113
adamovanja
closed
2 years ago
8
MAINT: add DOI badges
#112
misialq
closed
2 years ago
0
added description to readme
#111
nbokulich
closed
2 years ago
0
added biorxiv doi
#110
nbokulich
closed
2 years ago
0
Duplicated sections in tutorial
#109
adamovanja
closed
2 years ago
1
Scrape all ID types from paper collection
#108
adamovanja
closed
2 years ago
0
Scrape DOIs from web library collections
#107
adamovanja
closed
2 years ago
0
FIX: Check `NCBIAccessionIDs` for mixed type IDs
#106
adamovanja
closed
2 years ago
4
FIX: correct the sra install script link
#105
misialq
closed
2 years ago
3
FIX: force reinstallation of sra-tools packages
#104
adamovanja
closed
2 years ago
0
FIX: incorrect `install-sra-tools.sh` link for environment setup
#103
lina-kim
closed
2 years ago
0
ENH: fetch publication metadata with `get-metadata`
#102
nbokulich
closed
2 years ago
5
FIX: `make dev` requires manual approval to reinstall all packages
#101
adamovanja
closed
2 years ago
4
ENH: improve space check to better use available free space
#100
misialq
closed
2 years ago
3
ENH: Paper scraper
#99
adamovanja
closed
2 years ago
2
Action to scrape papers for IDs
#98
adamovanja
closed
2 years ago
0
FIX: add custom sra-tools installation script
#97
misialq
closed
2 years ago
2
Sra-tools do not work when installed via conda
#96
misialq
closed
2 years ago
2
Decouple fasterq-dump from prefetch to make processing of large datasets faster
#95
misialq
opened
2 years ago
0
FIX: prefetch downloads should be size-unlimited
#94
misialq
closed
2 years ago
0
Download of large samples is very slow
#93
misialq
closed
2 years ago
0
Logs are printed multiple times when fetching metadata
#92
misialq
opened
2 years ago
0
Downgrade missing sequence types warning to info
#91
lina-kim
opened
2 years ago
0
ENH: Parallelize sequence download and processing
#90
misialq
closed
2 years ago
2
Fetching even medium-large datasets takes ages
#89
misialq
closed
2 years ago
0
ENH: introduce NCBIAccessionIDs type
#88
misialq
closed
2 years ago
6
Add provenance for used accession IDs
#87
adamovanja
closed
2 years ago
1
FIX: extract missing experiment metadata
#86
misialq
closed
2 years ago
0
Experiment metadata is missing from the final result
#85
misialq
closed
2 years ago
0
ENH: do not fail on invalid IDs
#84
misialq
closed
2 years ago
5
Do not fail on invalid IDs
#83
misialq
closed
2 years ago
0
Adjust get-sequence's space limit
#82
misialq
opened
2 years ago
0
FIX: correctly extract run ids if only one item present in EFetch response
#81
misialq
closed
2 years ago
0
ENH: clean up prefetch files on success
#80
misialq
closed
2 years ago
1
FIX: use alternative spots location in run metadata
#79
misialq
closed
2 years ago
0
FIX: merge duplicated metadata columns
#78
misialq
closed
2 years ago
0
Use retmax param to better control fetching data
#77
misialq
closed
2 years ago
1
Filter get-sequences by criteria
#76
adamovanja
opened
2 years ago
0
MAINT: update copyright headers
#75
misialq
closed
2 years ago
0
ENH: added config instructions & logo draft
#74
adamovanja
closed
2 years ago
7
ENH: add combine-seqs action
#73
misialq
closed
2 years ago
2
FIX: report all failed IDs when storage exhausted
#72
misialq
closed
2 years ago
0
DOC: Tutorial
#71
LenaFloerl
closed
2 years ago
2
Fetching sequences fails sometimes when sra-tools are not configured properly
#70
misialq
closed
2 years ago
1
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