nf-core riboseq issues - Githubissues

nf-core / riboseq

Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.

https://nf-co.re/riboseq

MIT License

6 stars 4 forks source link

issues

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sample sheet condition column needs to be relevel with contrast information

#68 lpantano opened 1 month ago
0
Fixes #65

#67 evancofer opened 1 month ago
1
Translational efficiency analysis doesn't work when there are two conditions with less than three replicates

#66 Xinlei-Gao opened 2 months ago
0
Missing process or function BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME()

#65 progistar opened 3 months ago
0
NoSuchFileException: https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/rfam-5.8s-database-id98.fasta

#64 sopenaml opened 4 months ago
0
Important! Template update for nf-core/tools v2.14.1

#63 nf-core-bot closed 4 months ago
2
Important! Template update for nf-core/tools v2.14.0

#62 nf-core-bot closed 4 months ago
1
feat(metro-map): update metro map for better cohesion with rnaseq

#61 maxulysse closed 4 months ago
2
Empty ref to samtools sort

#60 JackCurragh closed 5 months ago
1
Supply empty reference for SAMTOOLS_SORT

#59 aostiles closed 5 months ago
0
Bumping to 1.1.0dev

#58 pinin4fjords closed 5 months ago
1
fixed svgs to match the exported pngs

#57 JackCurragh closed 5 months ago
1
Dev -> master for v1.0.1

#56 pinin4fjords closed 5 months ago
1
Prerelease v1.0.1

#55 pinin4fjords closed 5 months ago
1
Add legal logos and first metro map

#54 FelixKrueger closed 5 months ago
5
Bump to v1.0.1 and set Zenodo

#53 pinin4fjords closed 5 months ago
2
updated changelog

#52 JackCurragh closed 5 months ago
1
changed logos to the custom w/ ribosome

#51 JackCurragh closed 5 months ago
4
V1.0.0 release review fixes

#50 pinin4fjords closed 5 months ago
1
Fix CI

#49 pinin4fjords closed 5 months ago
2
Remove stub option from download in CI

#48 pinin4fjords closed 5 months ago
1
Dev -> master for v1.0.0

#47 pinin4fjords closed 5 months ago
1
Prerelease changes v1.0.0

#46 pinin4fjords closed 5 months ago
1
Update CI from rnaseq, strip unused rnaseq components

#45 pinin4fjords closed 5 months ago
1
Fix lack of fastqc in multiqc report

#44 pinin4fjords closed 5 months ago
2
Add translational efficiency analysis with anota2seq

#43 pinin4fjords closed 5 months ago
2
Add alignment based quantification with Salmon

#42 pinin4fjords closed 5 months ago
2
Amend credits statement

#41 FelixKrueger closed 6 months ago
1
Ribotricer orf prediction

#40 pinin4fjords closed 6 months ago
1
Integrate Ribo-TISH

#39 pinin4fjords closed 6 months ago
2
Important! Template update for nf-core/tools v2.13.1

#38 nf-core-bot closed 7 months ago
1
Altos star params

#37 pinin4fjords closed 7 months ago
1
Bump bbsplit module to prevent index overwrites

#36 pinin4fjords closed 7 months ago
1
Sortmerna: index once

#35 pinin4fjords closed 7 months ago
3
Fix order of preprocessing steps

#34 pinin4fjords closed 7 months ago
3
Optimise riboseq star

#33 pinin4fjords closed 7 months ago
1
Nf core template merge 2.13 (manual)

#32 pinin4fjords closed 7 months ago
3
URGENT: pin nf-validation version

#31 nvnieuwk opened 7 months ago
1
Optimise STAR command for riboseq data

#30 pinin4fjords opened 7 months ago
5
Important! Template update for nf-core/tools v2.13

#29 nf-core-bot closed 7 months ago
1
Generate contaminants file

#28 pinin4fjords opened 7 months ago
2
Add differential translation analysis

#27 pinin4fjords opened 7 months ago
0
Add translation efficiency analysis

#26 pinin4fjords opened 7 months ago
0
Add post-trimming fragment length check / reporting

#25 pinin4fjords opened 7 months ago
0
Incorporate check for 3nt periodicity

#24 pinin4fjords opened 7 months ago
4
Incorporate plastid metagene module

#23 pinin4fjords opened 7 months ago
0
Add plastid phase_by_size module

#22 pinin4fjords opened 7 months ago
0
Add psite estimation with plastid

#21 pinin4fjords closed 5 months ago
4
Assess ORF-rater for addition

#20 pinin4fjords closed 6 months ago
1
Add ribotricer detectorfs module

#19 pinin4fjords closed 5 months ago
1