nf-core/viralintegration issues and pull requests

#66 - Aligner choice in viralintegration pipeline

Issue - State: open - Opened by chirayug about 1 year ago
Labels: bug

#65 - Important! Template update for nf-core/tools v2.10

Pull Request - State: open - Opened by nf-core-bot about 1 year ago

#64 - Add support for single end reads

Issue - State: open - Opened by alyssa-ab over 1 year ago
Labels: enhancement

#63 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#62 - dev -> master for 0.1.1 release

Pull Request - State: closed - Opened by alyssa-ab over 1 year ago - 1 comment

#61 - Important! Template update for nf-core/tools v2.8

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#60 - Merge DOI from master

Pull Request - State: closed - Opened by alyssa-ab over 1 year ago - 1 comment

#59 - Organize into subworkflows

Pull Request - State: open - Opened by alyssa-ab over 1 year ago - 1 comment

#58 - Add subworkflows

Issue - State: open - Opened by alyssa-ab over 1 year ago
Labels: enhancement

#57 - bug fix: rollback star and samtools version

Pull Request - State: closed - Opened by alyssa-ab almost 2 years ago - 1 comment
Labels: bug

#56 - Add viRNAtrap to pipeline

Issue - State: open - Opened by allaway almost 2 years ago
Labels: enhancement

#55 - STAR Failure - roll back version

Issue - State: closed - Opened by alyssa-ab almost 2 years ago - 1 comment
Labels: bug

#54 - Dedup star args

Pull Request - State: open - Opened by Emiller88 almost 2 years ago - 1 comment

#53 - Processes to turn into a subworkflow

Issue - State: open - Opened by Emiller88 almost 2 years ago

#52 - dev -> master for 0.1.0 release

Pull Request - State: closed - Opened by alyssa-ab almost 2 years ago - 10 comments

#51 - v1.0.0 Release Criteria

Issue - State: open - Opened by Emiller88 almost 2 years ago
Labels: enhancement

#50 - Documentation push

Issue - State: closed - Opened by Emiller88 almost 2 years ago
Labels: enhancement

#49 - Prepare for v1.0.0

Pull Request - State: closed - Opened by alyssa-ab almost 2 years ago - 3 comments

#48 - Update documentation and add example analysis

Issue - State: open - Opened by lewynli almost 2 years ago
Labels: enhancement

#47 - Look into failing md5sums on CI

Issue - State: open - Opened by Emiller88 almost 2 years ago
Labels: bug

#46 - Check scripts are up-to-date before initial release

Issue - State: closed - Opened by Emiller88 almost 2 years ago

#45 - Important! Template update for nf-core/tools v2.7.2

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 2 comments

#44 - Pipeline terminated prematurely with Exception thrown in fastq_polyA_stripper.py

Issue - State: closed - Opened by lewynli almost 2 years ago - 2 comments
Labels: bug

#43 - Add nf-test

Pull Request - State: closed - Opened by Emiller88 almost 2 years ago - 3 comments

#42 - Important! Template update for nf-core/tools v2.7.1

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 2 comments

#41 - Multiqc

Pull Request - State: closed - Opened by alyssa-ab almost 2 years ago

#40 - Remove duplicates

Pull Request - State: closed - Opened by Emiller88 almost 2 years ago

#39 - Write basic nf-tests

Issue - State: closed - Opened by Emiller88 almost 2 years ago
Labels: enhancement

#38 - Finish Summary Report

Pull Request - State: closed - Opened by alyssa-ab about 2 years ago - 1 comment

#37 - Update test data for nf-test/summary_report

Issue - State: open - Opened by alyssa-ab about 2 years ago - 2 comments
Labels: enhancement

#36 - Update README.md

Pull Request - State: closed - Opened by leipzig about 2 years ago

#35 - Add local module labels

Issue - State: closed - Opened by Emiller88 about 2 years ago
Labels: enhancement

#34 - chimeric_contig / summary_report

Pull Request - State: closed - Opened by alyssa-ab about 2 years ago

#33 - Pass Index Files into ExtractChimericGenomicTargets

Issue - State: closed - Opened by alyssa-ab about 2 years ago
Labels: enhancement

#32 - Loop in results to multiqc

Issue - State: closed - Opened by Emiller88 about 2 years ago - 2 comments
Labels: enhancement

#31 - Use a small human reference for test data

Issue - State: closed - Opened by Emiller88 about 2 years ago - 5 comments
Labels: enhancement

#30 - STAR_VALIDATE / SummaryReport

Pull Request - State: closed - Opened by alyssa-ab about 2 years ago - 1 comment

#29 - ExtractEvidenceReads

Issue - State: closed - Opened by Emiller88 over 2 years ago - 1 comment
Labels: enhancement

#28 - SummaryReport

Issue - State: closed - Opened by Emiller88 over 2 years ago - 3 comments
Labels: enhancement

#27 - Genome plot doesn't output anything

Issue - State: closed - Opened by Emiller88 over 2 years ago
Labels: bug

#26 - Look into License

Issue - State: closed - Opened by Emiller88 over 2 years ago - 1 comment
Labels: help wanted, CTAT

#25 - Replace bamsifter with deepTools bamCoverage

Issue - State: open - Opened by Emiller88 over 2 years ago
Labels: enhancement

#24 - Virus report

Pull Request - State: closed - Opened by alyssa-ab over 2 years ago - 2 comments
Labels: CTAT

#23 - VirusReport

Issue - State: closed - Opened by Emiller88 over 2 years ago
Labels: enhancement

#22 - Virusinsertionsites

Pull Request - State: closed - Opened by alyssa-ab over 2 years ago - 2 comments

#21 - Use CTAT singularity image

Issue - State: open - Opened by Emiller88 over 2 years ago - 1 comment
Labels: enhancement

#20 - Add RemoveDuplicates

Issue - State: closed - Opened by Emiller88 over 2 years ago - 2 comments
Labels: enhancement, CTAT

#19 - Add cat_fasta process

Pull Request - State: closed - Opened by alyssa-ab over 2 years ago - 1 comment
Labels: CTAT

#18 - add trimmomatic module + specify qual_trim

Pull Request - State: closed - Opened by alyssa-ab over 2 years ago - 7 comments
Labels: CTAT

#17 - polyA_stripper script

Pull Request - State: closed - Opened by alyssa-ab over 2 years ago - 1 comment
Labels: CTAT

#16 - Star alignment

Pull Request - State: closed - Opened by Emiller88 over 2 years ago - 1 comment

#15 - CTAT-VIF lib integration subworkflow

Issue - State: closed - Opened by Emiller88 over 2 years ago
Labels: enhancement, CTAT

#14 - Blatbox

Pull Request - State: open - Opened by Emiller88 over 2 years ago - 1 comment

#13 - add nf-core module metaphlan3

Pull Request - State: closed - Opened by allaway over 2 years ago - 1 comment

#12 - Add test data

Pull Request - State: closed - Opened by Emiller88 over 2 years ago - 1 comment

#11 - Remove duplicates

Issue - State: closed - Opened by Emiller88 over 2 years ago
Labels: CTAT

#10 - InsertionSiteCandidates

Issue - State: closed - Opened by Emiller88 over 2 years ago - 1 comment
Labels: CTAT

#9 - PolyA_stripper

Issue - State: closed - Opened by Emiller88 over 2 years ago - 2 comments
Labels: CTAT

#8 - Trimmomatic

Issue - State: closed - Opened by Emiller88 over 2 years ago - 3 comments
Labels: CTAT

#7 - Virus Infection Evidence Viewer

Issue - State: closed - Opened by Emiller88 over 2 years ago - 1 comment
Labels: CTAT, output

#6 - Virus Insertion Viewer

Issue - State: closed - Opened by Emiller88 over 2 years ago - 1 comment
Labels: CTAT, output

#5 - Virus insertion site candidates and read counts

Issue - State: closed - Opened by Emiller88 over 2 years ago - 1 comment
Labels: CTAT, output

#4 - Add in STAR Alignment

Issue - State: closed - Opened by Emiller88 over 2 years ago - 1 comment
Labels: CTAT

#3 - Create dummy fastq data for testing

Issue - State: closed - Opened by allaway over 2 years ago - 2 comments
Labels: enhancement

#2 - Add MetaPhlAn 3.0 module

Issue - State: open - Opened by allaway over 2 years ago - 1 comment
Labels: enhancement

#1 - Add viral_fasta and index

Pull Request - State: closed - Opened by alyssa-ab over 2 years ago - 3 comments

GitHub / nf-core/viralintegration issues and pull requests