nf-core oncoanalyser issues

nf-core / oncoanalyser

A comprehensive cancer DNA/RNA analysis and reporting pipeline

https://nf-co.re/oncoanalyser

MIT License

26 stars 5 forks source link

issues

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Compatibility of IonTorrent BAM Files for HRD Analysis with nf-core/oncoanalyser

#92 Sadiki-Noureddine opened 5 days ago
0
Improve input validation for FASTQ

#91 scwatts opened 5 days ago
0
Update CHANGELOG.md

#90 scwatts closed 1 week ago
1
invalid file type: 'fastq'

#89 jkneppers closed 1 week ago
1
Fix software version reporting

#88 scwatts closed 2 weeks ago
1
Update PAVE somatic command

#87 scwatts closed 2 weeks ago
1
Add missing conda directive to MarkDups process

#86 scwatts closed 3 weeks ago
1
Release 1.0.0

#85 scwatts closed 6 days ago
1
Add documentation describing workflow design choices

#84 scwatts opened 3 weeks ago
0
Implement basic sequence and alignment QC reporting

#83 scwatts opened 3 weeks ago
0
Determine whether certain Groovy syntax should be removed

#82 scwatts opened 3 weeks ago
0
Reintroduce MultiQC for workflow and analysis summary

#81 scwatts opened 3 weeks ago
0
Add reference data to iGenomes

#80 scwatts opened 3 weeks ago
0
Determine future feasibility of switch to nf-core bump-version

#79 scwatts opened 3 weeks ago
0
Fix panel parameter validation during pre-flight check

#78 scwatts closed 3 weeks ago
1
Setting targeted mode without a panel gives an error message containing null

#77 SPPearce closed 3 weeks ago
1
Allow RNA BAM from samplesheet as LILAC input

#76 scwatts closed 3 weeks ago
1
Move fastp arguments to modules.config

#75 SPPearce opened 1 month ago
2
Eliminate bottlenecking of markdups

#74 SPPearce opened 1 month ago
1
UMI support in WGTS mode

#73 SPPearce opened 1 month ago
1
Apply the seventh set of reviewer recommendations

#72 scwatts closed 1 month ago
5
Shrink reference data to support execution on GHA runners

#71 FriederikeHanssen opened 1 month ago
1
Apply the sixth set of reviewer recommendations

#70 scwatts closed 1 month ago
1
Update documentation in usage.md

#69 scwatts closed 1 month ago
1
Apply the fifth set of reviewer recommendations

#68 scwatts closed 1 month ago
1
Apply the fourth set of reviewer recommendations

#67 scwatts closed 1 month ago
1
Add support for custom targeted panel

#66 bounlu opened 1 month ago
1
`samplesheet` format is not recognised

#65 bounlu closed 1 month ago
6
Apply the third set of reviewer recommendations

#64 scwatts closed 1 month ago
1
Gene fusion detection

#63 bounlu closed 1 month ago
3
Apply the second set of reviewer recommendations

#62 scwatts closed 1 month ago
1
Correct Nextflow schema entry for Isofox read length

#61 scwatts closed 2 months ago
1
isofox_read_length does not have a 'type' attribute

#60 alexiswl closed 2 months ago
0
Use correct MarkDups version in Conda env and documentation URL

#59 scwatts closed 2 months ago
1
Bump SAGE to 3.4.4

#58 scwatts closed 2 months ago
1
Bump AMBER to 4.0.1

#57 scwatts closed 2 months ago
1
Correct read processing subworkflow optional output channel

#56 scwatts closed 2 months ago
1
Markdup doesn't accept unpaired reads aligned with minimap2

#55 charlenelawdes closed 1 month ago
2
symlink specific gridss index files

#54 casslitch closed 2 months ago
10
Fix directory shadowing symlinks

#53 scwatts closed 2 months ago
1
Bump MarkDups to 1.1.7

#52 scwatts closed 3 months ago
1
Migrate from nf-validation to nf-schema

#51 scwatts opened 3 months ago
0
Assess suitability of local modules for transfer to nf-core/modules

#50 scwatts opened 3 months ago
0
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