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NationalGenomicsInfrastructure
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piper
A genomics pipeline build on top of the GATK Queue framework
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.done file generated but its not done
#38
parlundin
opened
9 years ago
4
Qualimap: add parameter for comparing GC content distribution with the reference
#37
ewels
closed
9 years ago
1
UPPMAX: Memory overflow error
#36
parlundin
closed
9 years ago
4
setupFileCreator return code is 0 even if it fails
#35
mariogiov
closed
9 years ago
3
Change default path to resource file to ua-sthlm communal project
#34
johandahlberg
closed
9 years ago
0
Commandline option in setupFileCreator to specify qos is missing
#33
johandahlberg
closed
9 years ago
0
Haloplex script needs update to new way of fetching resources
#32
johandahlberg
opened
9 years ago
0
setupFileCreator regex bug
#31
mariogiov
closed
9 years ago
1
Piper return code
#30
vezzi
closed
9 years ago
4
FastQC added into Piper
#29
johandahlberg
opened
9 years ago
2
Change the pipeline setup xml to some more "flexible" solution
#28
johandahlberg
closed
9 years ago
8
Add concordance check with snp-genotyping
#27
johandahlberg
closed
9 years ago
3
fc_id naming convention and stckh2UUSNPSEQ
#26
vezzi
closed
9 years ago
1
sthlm2UUSNP NoClassDefFound
#25
mariogiov
closed
9 years ago
3
Fall back to copying instead of hard linking
#24
johandahlberg
opened
9 years ago
0
Report of versions
#23
jessieno
closed
9 years ago
2
sthlm2UUSNP problem on M.Kaller
#22
vezzi
closed
9 years ago
17
Running piper on M.Kaller_14_06
#21
vezzi
closed
9 years ago
7
sthlm2UUSNP problem with dual-indexing
#20
vezzi
closed
9 years ago
2
Update to GATK version 3.2-2
#19
johandahlberg
closed
9 years ago
1
SetupFileCreator problem
#18
vezzi
closed
9 years ago
5
sthlm2UUSNP and four-tier directory format
#17
mariogiov
closed
9 years ago
12
Qualimap fails
#16
vezzi
closed
9 years ago
3
Piper fails after last update
#15
vezzi
closed
9 years ago
1
report.tsv is not overwritten when sthlm2UUSNP is run
#14
mariogiov
closed
9 years ago
2
Don't die if the files are present in Sthlm2UUSNP
#13
johandahlberg
closed
9 years ago
4
final report fails
#12
vezzi
closed
9 years ago
1
Lower compression levels for output files
#11
johandahlberg
closed
9 years ago
2
Update to GATK 3.2
#10
johandahlberg
closed
9 years ago
3
Qulimap dies without reporting non-zero exit status back to piper
#9
johandahlberg
closed
9 years ago
5
preliminary_alignment_qc report generation fails
#8
vezzi
closed
9 years ago
2
Renaming output folders
#7
vezzi
closed
9 years ago
3
Directory tree switch
#6
mariogiov
closed
9 years ago
6
Running piper
#5
vezzi
closed
10 years ago
3
Problem with java module (maybe nestor problem?)
#4
vezzi
closed
10 years ago
1
Problem with sthlm2UUSNP
#3
vezzi
closed
10 years ago
16
Missing resources when running from path
#2
johandahlberg
closed
10 years ago
2
sthlm2UUSNP misses files
#1
johandahlberg
closed
10 years ago
0
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