SciLifeLab/NGI-RNAseq
Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
GroovyMIT
Issues
- 1
Conflict with user Python libraries
#237 opened by pareng - 7
Add optional UMI handling
#145 opened by ewels - 2
Add warning to the top of MultiQC reports if samples are skipped due to low alignment
#139 opened by ewels - 1
Save BAM index file
#134 opened by ewels - 2
Look into adding RSEM
#132 opened by ewels - 1
Show good / bad examples in documentation
#93 opened by Hammarn - 5
Error: not enough memory for BAM sorting
#234 opened by Zeinab5 - 2
STAR error when running with extra command line flags
#221 opened by Hammarn - 37
Problems running on cs3e Hebbe
#174 opened by JohnHellgren - 2
edgeR_heatmap_MDS.r: duplicated column name(s)
#235 opened by omerfaruk84 - 2
ERROR ~ Unknown config attribute: igenome_base
#233 opened by mhebrard - 1
IDEA: DOIs for repository
#188 opened by apeltzer - 2
genome configuration file
#236 opened by PycnopodiaD - 1
Library strandedness
#231 opened by Zeinab5 - 2
ERROR: Failed to invoke
#230 opened by Zeinab5 - 11
no exon lines in the GTF file
#229 opened by Zeinab5 - 1
Discard very short reads from trimming
#228 opened by ewels - 6
- 3
- 0
Memory requirement for local jobs too high
#192 opened by orzechoj - 0
RSeQC version statement not updated
#215 opened by ewels - 1
Dockerfile contains wrong path for conda environment
#222 opened by zichner - 1
Dockerfile Typo
#219 opened by apeltzer - 3
- 1
Revert dodgy STAR alignment parameter
#212 opened by ewels - 1
Specify MultiQC modules to run
#207 opened by ewels - 1
STAR Index Generation
#211 opened by apeltzer - 1
Biotypes issues
#210 opened by apeltzer - 2
biotypes chart showing only last 7 entries
#198 opened by jakubovciak - 1
- 1
Use MultiQC Custom Content for script output
#136 opened by ewels - 2
Collect software versions
#138 opened by ewels - 4
GFF file input
#184 opened by JohnHellgren - 2
MultiQC doesn't run when there is only one sample
#180 opened by ewels - 12
Test data URL will go down soon
#195 opened by ewels - 6
Bug report: address 0x6, cause 'memory not mapped' error in the sample_correlation process
#157 opened by chuan-wang - 26
- 1
Update the Docs
#150 opened by Hammarn - 4
Optional merge process?
#98 opened by ewels - 2
- 3
Refactor/benchmark the RSeQC process
#92 opened by Hammarn - 2
trim_glore cannot find fastq files
#144 opened by MIAOKUI - 2
New --help option
#102 opened by ewels - 8
Cannot download/upload from s3 within nextflow
#153 opened by danielecook - 2
Add optional fastq-screen step
#142 opened by Hammarn - 1
Merge featureCounts needs Python on UPPMAX
#133 opened by ewels - 2
Running with custom reference does not produce output, but claims successful run
#131 opened by varemo - 6
threads management and single node of toy configuration of Torque in the local machine?
#120 opened by zhenyisong - 5
strandness parameter? ----strandRule '1++,1--,2+-,2-+' similar to --forward_stranded
#114 opened by zhenyisong - 0
Update to latest StringTie version
#94 opened by Hammarn