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SciLifeLab
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NGI-RNAseq
Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
https://ngisweden.scilifelab.se/
MIT License
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Conflict with user Python libraries
#237
pareng
closed
6 years ago
1
genome configuration file
#236
PycnopodiaD
closed
6 years ago
2
edgeR_heatmap_MDS.r: duplicated column name(s)
#235
omerfaruk84
closed
6 years ago
2
Error: not enough memory for BAM sorting
#234
Zeinab5
closed
6 years ago
5
ERROR ~ Unknown config attribute: igenome_base
#233
mhebrard
closed
6 years ago
2
Make use of multiqc general stat table
#232
senthil10
closed
6 years ago
2
Library strandedness
#231
Zeinab5
closed
6 years ago
1
ERROR: Failed to invoke
#230
Zeinab5
closed
6 years ago
2
no exon lines in the GTF file
#229
Zeinab5
closed
6 years ago
11
Discard very short reads from trimming
#228
ewels
closed
6 years ago
1
Add the pipeline version to the container tag
#227
ewels
closed
6 years ago
0
Bump pipeline version to v1.4
#226
ewels
closed
6 years ago
0
Drop max_mem to 6.GB for travis tests.
#225
ewels
closed
6 years ago
0
Tidied up more straggler docs
#224
ewels
closed
6 years ago
0
Update changelog and docs
#223
ewels
closed
6 years ago
0
Dockerfile contains wrong path for conda environment
#222
zichner
closed
6 years ago
1
STAR error when running with extra command line flags
#221
Hammarn
closed
6 years ago
2
Update offline docs to recommend pulling a tagged container
#220
arontommi
closed
6 years ago
6
Dockerfile Typo
#219
apeltzer
closed
6 years ago
1
Testing and fixing new docker image.
#218
ewels
closed
6 years ago
7
Use the latest version of conda
#217
ewels
closed
6 years ago
1
Rewrote docker container using bioconda environment.yml
#216
ewels
closed
6 years ago
3
RSeQC version statement not updated
#215
ewels
closed
6 years ago
0
Use fixed container URI
#214
apeltzer
closed
6 years ago
6
Removed non-default option from star
#213
apeltzer
closed
6 years ago
0
Revert dodgy STAR alignment parameter
#212
ewels
closed
6 years ago
1
STAR Index Generation
#211
apeltzer
closed
6 years ago
1
Biotypes issues
#210
apeltzer
closed
6 years ago
1
Problems without specific revision of pipeline when pulling via Singularity
#209
apeltzer
closed
6 years ago
3
Only use our specific modules for MultiQC
#208
Hammarn
closed
6 years ago
3
Specify MultiQC modules to run
#207
ewels
closed
6 years ago
1
Use all biotypes
#206
Hammarn
closed
6 years ago
0
Minor rewrite of the docs for --min_aln_length
#205
ewels
closed
6 years ago
0
added minimal alignment lenghts to avoid soft-clipping artifacts
#204
Hammarn
closed
6 years ago
0
Add option to specify strand direction for dupradar script
#203
rfenouil
closed
6 years ago
1
Don't use uppmax.config for uppmax-modules.config
#202
ewels
closed
6 years ago
5
Avoid filename truncation in dupradar.r (+remove detectcores)
#201
rfenouil
closed
6 years ago
2
Container path not expanded properly with Singularity on Uppmax
#200
Hammarn
closed
6 years ago
3
Add RSeQC version number to report
#199
rfenouil
closed
6 years ago
1
biotypes chart showing only last 7 entries
#198
jakubovciak
closed
6 years ago
2
Fix the tests since webexport file hosting is no longer available.
#197
Hammarn
closed
6 years ago
4
Bunch of minor tweaks / version refactor / MultiQC fix
#196
ewels
closed
6 years ago
7
Test data URL will go down soon
#195
ewels
closed
6 years ago
12
QBIC Configuration Updates
#194
apeltzer
closed
6 years ago
1
Add Singularity testing to Travis CI
#193
maxulysse
closed
6 years ago
4
Memory requirement for local jobs too high
#192
orzechoj
closed
6 years ago
0
Fix RSeQC filename errors for MultiQC
#191
ewels
closed
6 years ago
1
Defer execution of the docker tag version.
#190
ewels
closed
6 years ago
3
Minor docs tweaks
#189
ewels
closed
6 years ago
2
IDEA: DOIs for repository
#188
apeltzer
closed
6 years ago
1
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