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nf-core
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oncoanalyser
A comprehensive cancer DNA/RNA analysis and reporting pipeline
https://nf-co.re/oncoanalyser
MIT License
39
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6
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Apply the first set of reviewer recommendations
#49
scwatts
closed
3 months ago
1
Bump bwa-mem2 container build
#48
scwatts
closed
3 months ago
1
Bump SvPrep to 1.2.4
#47
scwatts
closed
3 months ago
1
Bump Sambamba to 1.0.1
#46
scwatts
closed
3 months ago
0
Bump MarkDups 1.1.5 to Bioconda build hdfd78af_1
#45
scwatts
closed
3 months ago
0
task: name=NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_RNA:STAR (1); work-dir=null
#44
taijiyamazoe
closed
3 months ago
8
Use all available threads for fastp process
#43
scwatts
closed
3 months ago
1
Fix conditional creation of bwa-mem2 index
#42
scwatts
closed
3 months ago
1
Make README.md admonition compatible with website
#41
scwatts
closed
3 months ago
1
Fix display of the ORANGE report screencap on the nf-core website
#40
scwatts
closed
3 months ago
1
Change admonition style to fix usage docs rendering
#39
scwatts
closed
3 months ago
1
Add known issue section to README.md
#38
scwatts
closed
3 months ago
1
MarkDups error processing hard-clipped supplementary alignments
#37
scwatts
closed
2 months ago
2
Do not split FASTQs during tests
#36
scwatts
closed
4 months ago
1
Remove duplicate tests
#35
scwatts
closed
4 months ago
1
Rename bwa-mem2 index variables
#34
scwatts
closed
4 months ago
2
Remove unused reference parameters from the test_stub profile
#33
scwatts
closed
4 months ago
1
Fix 'download_pipeline.yml' GHA workflow
#32
scwatts
closed
4 months ago
0
Update CITATIONS.md
#31
scwatts
closed
4 months ago
1
Error when using bam files without 'chr'
#30
PaulaOteroS
closed
3 months ago
2
Initial release review [DO NOT MERGE]
#29
scwatts
closed
1 month ago
4
Fix dev branch root commit
#28
scwatts
closed
4 months ago
1
Use simulated data for pipeline tests
#27
scwatts
closed
4 months ago
1
Bump SAGE to 3.4.3
#26
scwatts
closed
4 months ago
1
Apply formatting fixes and other minor fixes
#25
scwatts
closed
4 months ago
0
Important! Template update for nf-core/tools v2.14.1
#24
nf-core-bot
closed
4 months ago
1
Important! Template update for nf-core/tools v2.14.0
#23
nf-core-bot
closed
4 months ago
2
virusbreakend gridsscache file exists
#22
iagooteroc
closed
4 months ago
9
Set bwa-mem2 batch size for reproducibility
#21
scwatts
closed
3 months ago
5
Adjustments to better match nf-core standards
#20
scwatts
closed
4 months ago
1
Improve the prepare reference workflow
#19
scwatts
closed
4 months ago
1
Correct mistake in assets/samplesheet.csv
#18
scwatts
closed
4 months ago
1
Mistake in example sample sheet
#17
casslitch
closed
4 months ago
1
Refactor reference data parameters
#16
scwatts
closed
4 months ago
1
Improve GHA CI workflow step name
#15
scwatts
closed
4 months ago
1
Update reference data URLs
#14
scwatts
closed
4 months ago
1
Missing output file(s) `WGS_20M_A375.gridss.vcf.gz` expected by process `NFCORE_ONCOANALYSER:WGTS:GRIDSS_SVPREP_CALLING:DEPTH_ANNOTATOR (WGS_20M_A375)`
#13
PFRoux
closed
4 months ago
13
Use fixed GRIDSS container for VIRUSBreakend
#12
scwatts
closed
5 months ago
1
Busybox error
#11
mich-chan
closed
5 months ago
6
Linting in nf-core tools appears to require that params are set in nextflow.config and nextflow_schema.json
#10
scwatts
closed
4 months ago
1
Add basic nf-core documentation
#9
scwatts
closed
4 months ago
4
Implement Neo subworkflow
#8
scwatts
closed
3 months ago
4
Fix all GHA linting
#7
scwatts
closed
6 months ago
1
Implement alignment subworkflow
#6
scwatts
closed
4 months ago
2
Complete basic nf-core documentation
#5
scwatts
closed
4 months ago
0
Implement required tests
#4
scwatts
closed
4 months ago
0
Important! Template update for nf-core/tools v2.13.1
#3
nf-core-bot
closed
6 months ago
2
Add low coverage filter settings for SAGE
#2
jaesvi
closed
6 months ago
5
Refactor data flow and channel logic
#1
scwatts
closed
10 months ago
0
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