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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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MAINT: adjust copyright year
#69
misialq
closed
2 years ago
0
Action to merge multiple sequences of same sequencing runs
#68
adamovanja
closed
2 years ago
0
FIX: Space limit & number of retries
#67
adamovanja
closed
2 years ago
0
FIX: properly use prefetch results while calling fasterq-dump
#66
misialq
closed
2 years ago
0
FIX: raise error when no sequences present
#65
misialq
closed
2 years ago
1
ENH: adding space exhaustion break
#64
adamovanja
closed
2 years ago
1
No retries in case of space issue
#63
adamovanja
closed
2 years ago
0
Save fetched sequences before space issue
#62
adamovanja
closed
2 years ago
0
Raise error when no sequences present
#61
misialq
closed
2 years ago
0
Action to estimate `get-sequences` space requirement
#60
adamovanja
opened
2 years ago
3
FIX: Change description in progress bar
#59
adamovanja
closed
2 years ago
1
Silent exits in non-verbose mode
#58
adamovanja
closed
2 years ago
6
ENH: use progress bar to display download progress
#57
misialq
closed
2 years ago
0
FIX: gracefully exit on uncaught errors in entrezpy threads
#56
misialq
closed
2 years ago
0
ENH: add action to merge multiple metadata
#55
misialq
closed
2 years ago
1
ENH: output a list of failed IDs
#54
misialq
closed
2 years ago
0
ENH: Adding prefetch before fasterq-dump
#53
adamovanja
closed
2 years ago
2
Output a list of failed IDs from `get-sequences`
#52
misialq
closed
2 years ago
8
Prefetch prior to fasterq-dump in get-sequences
#51
adamovanja
closed
2 years ago
0
Capturing gaierror of entrezpy
#50
adamovanja
closed
2 years ago
0
DOC: Tutorial
#49
LenaFloerl
closed
2 years ago
3
FIX: update sra-tools version
#48
adamovanja
closed
3 years ago
1
`fasterq-dump` differing output for ProjectID member and runID
#47
adamovanja
closed
3 years ago
3
FIX: readme update
#46
adamovanja
closed
3 years ago
4
MAINT: update citations
#45
misialq
closed
3 years ago
0
FIX: Error raising in get-sequences
#44
adamovanja
closed
3 years ago
0
`get-sequences` produces variable output
#43
adamovanja
closed
3 years ago
0
FIX: method descriptions
#42
adamovanja
closed
3 years ago
2
ENH: Add logging ability
#41
misialq
closed
3 years ago
0
ENH: allow project IDs in get-sequences
#40
misialq
closed
3 years ago
0
get-sequences should also be able to fetch by project ID
#39
misialq
closed
3 years ago
0
FIX: simplify run creation
#38
misialq
closed
3 years ago
0
FIX: retry fetching missing runs
#37
misialq
closed
3 years ago
0
get-metadata KeyError & hangs
#36
adamovanja
closed
3 years ago
0
get-metadata IndexError & hangs
#35
adamovanja
closed
3 years ago
0
DOC: usage tutorial
#34
LenaFloerl
closed
3 years ago
1
Fetch data by StudyID
#33
adamovanja
closed
2 years ago
1
Fetching large amounts of runs fails
#32
misialq
closed
3 years ago
1
Update diagram on fetching metadata
#31
adamovanja
closed
2 years ago
2
MAINT: GHA should at least run the tests
#30
misialq
closed
3 years ago
0
Data fetching by BioProject ID
#29
misialq
closed
3 years ago
3
Replace input list with file of IDs
#28
lina-kim
closed
3 years ago
1
Make Entrez logging configurable
#27
misialq
closed
3 years ago
0
Efetch module refactor
#26
misialq
closed
3 years ago
6
sample_id param name may be confusing
#25
misialq
closed
3 years ago
0
Fetching metadata by sample ID never returns
#24
misialq
closed
3 years ago
0
Add citations to all methods
#23
misialq
closed
3 years ago
0
FIX: do not error on duplicated metadata keys
#22
misialq
closed
3 years ago
0
Duplicated metadata keys are not handled correctly
#21
misialq
closed
3 years ago
1
Chaining sequence and metadata fetching
#20
adamovanja
closed
3 years ago
0
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