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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: use tempfiles in tests
#169
misialq
closed
1 month ago
1
DEV: 2024.10
#168
nbokulich
closed
5 months ago
0
MAINT: update installation instructions
#167
adamovanja
closed
4 months ago
3
MAINT: update install instructions
#166
nbokulich
closed
4 months ago
0
CI: update the distro
#165
misialq
closed
7 months ago
1
MAINT: remove the Rust dependency
#164
misialq
closed
9 months ago
5
ENH: add automated Docker image builds
#163
misialq
opened
10 months ago
1
CI: update to the newest version
#162
misialq
closed
11 months ago
1
FIX: Pandas deprecations
#161
adamovanja
closed
11 months ago
2
Deprecated pandas usage in `get-all` and in `get-ids-from-query`
#160
adamovanja
closed
11 months ago
0
Integrate automated image generation for new QIIME 2 releases
#159
lina-kim
opened
11 months ago
0
Add minimal Docker image for q2-fondue
#158
lina-kim
closed
11 months ago
5
Error when downloading data from NCBI
#157
vgenisel
closed
1 year ago
3
ENH: Fetch restricted access sequences with a repository key
#156
adamovanja
closed
1 year ago
4
Fetch restricted access sequences with a repository key
#155
adamovanja
closed
1 year ago
0
Temporary plugin error with no response
#154
adamovanja
opened
1 year ago
0
ENH: Add scraper sync note
#153
adamovanja
closed
1 year ago
1
FIX: remove original sequences after gzipping
#152
misialq
closed
1 year ago
1
Delete raw sequences after compression
#151
valentynbez
closed
1 year ago
4
Update QIIME 2 versions in README
#150
lina-kim
closed
1 year ago
2
FIX: Sequences mismatch
#149
adamovanja
closed
1 year ago
2
Mismatched sequences when both single and paired reads available per run ID
#148
adamovanja
closed
1 year ago
0
FIX: metadata should only retain the runs that were requested
#147
misialq
closed
1 year ago
2
ENH: add more installation instructions
#146
adamovanja
closed
1 year ago
1
MAINT: update DOI badge
#145
misialq
closed
2 years ago
1
MAINT: update citations
#144
misialq
closed
2 years ago
2
Update citation information
#143
nbokulich
closed
2 years ago
0
unzip tutorial
#142
nbokulich
closed
2 years ago
1
ENH: Highlight downstream analysis outside of Q2
#141
adamovanja
closed
2 years ago
2
MAINT: update installation instructions to use conda
#140
misialq
closed
2 years ago
1
ENH: improve data copy/gzip process after fetching fastq sequences
#139
misialq
closed
2 years ago
3
MAINT: simplify coverage testing in the CI
#138
misialq
closed
2 years ago
1
Raise warning when no run IDs are linked to aggregate ID
#137
adamovanja
opened
2 years ago
2
ENH: add an action to search for run IDs using a text query
#136
misialq
closed
2 years ago
1
FIX: correct E-Direct param setting when fetching metadata
#135
misialq
closed
2 years ago
1
Return already fetched metadata upon connection error
#134
adamovanja
opened
2 years ago
0
FIX: Correctly scraping accessions with whitespace characters
#133
adamovanja
closed
2 years ago
1
Process runs out of threads when fetching large amounts of metadata
#132
misialq
closed
2 years ago
2
FIX: add SRA Toolkit configuration step
#131
misialq
closed
2 years ago
1
SRA Toolkit still not properly configured after installation
#130
misialq
closed
2 years ago
4
ENH: Option to preserve DOI names when refetching with `failed_runs`
#129
adamovanja
closed
2 years ago
2
Fetch SRA IDs based on a search query
#128
misialq
closed
2 years ago
1
Validate BioProject IDs and Co. before fetching associated Run IDs
#127
adamovanja
opened
2 years ago
0
FIX: correctly install sra-toolkit during conda build
#126
misialq
closed
2 years ago
1
ENH: Improved metadata fetching and error logging
#125
adamovanja
closed
2 years ago
2
ENH: Scrape hyphenated ID sequences
#124
adamovanja
closed
2 years ago
1
`--o-failed-runs` remains empty after running `get-metadata` with missing run IDs
#123
adamovanja
closed
2 years ago
14
ENH: Full support sample and experiment IDs
#122
adamovanja
closed
2 years ago
2
FIX: Hiding Zotero user info
#121
adamovanja
closed
2 years ago
2
MAINT: CI improvements
#120
misialq
closed
2 years ago
1
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