HenrikBengtsson CostelloPSCNSeq issues

HenrikBengtsson / CostelloPSCNSeq

R package: Parent-specific Copy-number Estimation Pipeline using HT-Seq Data

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issues

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Project folder out of date

#32 HenrikBengtsson opened 3 years ago
1
1.mpileup: Pathname not found

#31 ivan108 opened 3 years ago
8
resolve(..., value) is depreciated

#30 HenrikBengtsson closed 3 years ago
0
future.batchtools not connecting to Torque server

#29 ivan108 closed 3 years ago
4
Use another exome kit?

#28 HenrikBengtsson opened 3 years ago
10
TIPCC: annotationData -> /cbc/data,public/annotationData is broken

#27 HenrikBengtsson closed 3 years ago
4
qselect: cannot connect to server

#26 ivan108 closed 3 years ago
1
Pipeline does not work with sequenza (>= 3.0.0)

#25 HenrikBengtsson closed 5 years ago
0
ROBUSTNESS: Use '/usr/bin/env bash' shebangs

#23 HenrikBengtsson closed 5 years ago
0
DOCS: Add PMC numbers with URLs for all references

#22 HenrikBengtsson closed 5 years ago
0
DOCS: Clarify which steps require tumor-normal pairs

#21 HenrikBengtsson closed 5 years ago
0
Add assertion that BAM index files exist

#20 HenrikBengtsson closed 5 years ago
3
4.reports.pbs crashing

#19 ivan108 opened 5 years ago
8
Make 0.setup.R agile to config.yml

#18 HenrikBengtsson opened 5 years ago
3
Fixed path

#17 ivan108 closed 5 years ago
5
Issue loading required packages using README.md instructions

#16 SRHilz closed 6 years ago
2
Patient260 Incomplete Chromosome Coverage

#15 SRHilz closed 6 years ago
16
1.mpileup.R - BatchtoolsError write permission error

#14 SRHilz opened 6 years ago
5
POTENTIAL BUG: Lack of newline at end of sampleData/samples.tsv cause 3.pscbs.R to fail

#13 HenrikBengtsson closed 7 years ago
3
1.mpileup.R: Warning messages

#12 SRHilz closed 7 years ago
1
Version 0.3.0 of pipeline released

#11 HenrikBengtsson closed 7 years ago
2
Chr 1-25: Need to increase to `vmem=2gb` in .future.R

#10 HenrikBengtsson closed 7 years ago
1
TROUBLESHOOT: 3.pcsbs.R

#9 HenrikBengtsson closed 7 years ago
2
BUG: 1.mpileup.R gives Error: length(work) == length(todo) is not TRUE

#8 HenrikBengtsson closed 7 years ago
3
Proper chromosome tags (e.g. `chrs=1-22,X`) in several places

#7 HenrikBengtsson closed 7 years ago
1
added info to obtain required torque template

#6 SRHilz closed 7 years ago
2
Failing to run `1.mpileup.R`

#5 HenrikBengtsson closed 7 years ago
15
DOCS: Add installation instructions

#4 HenrikBengtsson closed 7 years ago
0
WISH: Add `--cleanup` to each script / step (was 5.cleanup.R)

#3 HenrikBengtsson opened 7 years ago
3
Turn these scripts into an R package

#2 HenrikBengtsson opened 7 years ago
0
1.mpileup.R gives error

#1 HenrikBengtsson closed 7 years ago
18