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SystemsGenetics
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GEMmaker
A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
https://gemmaker.readthedocs.io/en/latest/
MIT License
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Support for larger genomes
#239
fmobegi
opened
3 years ago
4
GEMmaker will not retry download_runs.py
#238
JohnHadish
closed
3 years ago
2
Easy RE-start on Failed runs
#237
JohnHadish
closed
2 months ago
2
failed_runs.metadata.txt in results directory
#236
JohnHadish
closed
2 years ago
2
Preliminary files clean-up not working
#235
fmobegi
closed
3 years ago
6
Kallisto exit code 1
#234
spficklin
closed
3 years ago
5
Running on Back queue
#233
JohnHadish
closed
2 years ago
2
Nextflow/GEMmaker does not automatically pull new material
#232
JohnHadish
closed
3 years ago
2
--max_cpus cannot be set from command line
#231
JohnHadish
closed
3 years ago
1
Information about setting singularity/docker cache dir
#230
JohnHadish
closed
3 years ago
1
Merging dev for 2.0 release.
#229
spficklin
closed
3 years ago
0
Fixes for the Ath26 dataset
#228
spficklin
closed
3 years ago
0
Main tweaks
#227
spficklin
closed
3 years ago
2
Exit code 141 on get_software_versions
#226
spficklin
closed
3 years ago
1
Added -b flag for kallisto
#225
spficklin
closed
3 years ago
0
GEM ordering
#224
JohnHadish
closed
3 years ago
2
Config tweaks
#223
spficklin
closed
3 years ago
1
Update installation.rst
#222
spficklin
closed
3 years ago
0
Documentation for dev branch (currently nf-core branch) does not have install information
#221
JohnHadish
closed
3 years ago
1
Updated Error messages to make them relevant to nf-core, spelling
#220
JohnHadish
closed
3 years ago
2
Home directory reference "~/" not recognized
#219
JohnHadish
closed
3 years ago
2
FASTQ file name should not require a _1 or _2 suffix
#218
spficklin
closed
3 years ago
3
Minor fix to correct lack of Salmon in MultiQC report
#217
spficklin
closed
3 years ago
1
Fix for issue #214
#216
bentsherman
closed
3 years ago
1
DSL2 compatiblity
#215
spficklin
closed
3 years ago
1
Gemmaker cannot pull SRA datasets
#214
feltus
closed
3 years ago
8
nf-core compatibility
#213
spficklin
closed
3 years ago
2
HRES nextflow configuration
#212
CandyH23
closed
3 years ago
6
Rerunning with different aligners
#211
spficklin
closed
3 years ago
1
Fix for Trimmomatic quality parameter
#210
spficklin
closed
3 years ago
4
Singularity cache directory not defined
#209
JohnHadish
closed
3 years ago
3
Remove main-e2e.nf
#208
bentsherman
closed
3 years ago
1
nf-core compliance
#207
spficklin
closed
3 years ago
7
Do we still need main-e2e.nf?
#206
spficklin
closed
3 years ago
3
Configuration and Organization Changes
#205
spficklin
closed
3 years ago
9
Fixes for multiple issues with SRAs
#204
spficklin
closed
3 years ago
11
output log has issues
#203
JohnHadish
closed
3 years ago
1
`clean_work_files.sh` fails on restart
#202
JohnHadish
closed
3 years ago
1
GEM naming convention needs change
#201
JohnHadish
closed
3 years ago
4
Remove singularity cache dir setting
#200
bentsherman
closed
3 years ago
1
GEMmaker should not need to be cloned every time it is ran
#199
JohnHadish
closed
3 years ago
3
nextflow.config is too long
#198
JohnHadish
closed
3 years ago
1
GEMmaker works with Nextflow 20.10.0 and Singularity 3.7.0
#197
feltus
closed
3 years ago
1
Docker Images throw error of "implausibly old timestamp"
#196
JohnHadish
closed
3 years ago
2
process fastqc_1 not included in output
#195
JohnHadish
closed
3 years ago
1
Created 'local' label for local processes
#194
bentsherman
closed
3 years ago
1
Cleanup Troubles
#193
spficklin
closed
3 years ago
1
MetaData
#192
spficklin
closed
3 years ago
6
GZ FASTQ files cause problems
#191
fmobegi
closed
3 years ago
9
What is the deal with the GEMmaker staging directory
#190
bentsherman
closed
3 years ago
8
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