Ecosyste.ms: Issues

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GitHub / nf-core/clipseq issues and pull requests

#110 - Important! Template update for nf-core/tools v2.13.1

Pull Request - State: open - Opened by nf-core-bot 9 months ago

#109 - Important! Template update for nf-core/tools v2.13

Pull Request - State: closed - Opened by nf-core-bot 9 months ago - 1 comment

#108 - Important! Template update for nf-core/tools v2.12

Pull Request - State: closed - Opened by nf-core-bot 10 months ago - 1 comment

#107 - Important! Template update for nf-core/tools v2.11.1

Pull Request - State: closed - Opened by nf-core-bot 11 months ago - 1 comment

#106 - Important! Template update for nf-core/tools v2.11

Pull Request - State: closed - Opened by nf-core-bot 11 months ago - 1 comment

#105 - refactor sample sheets to enable group and input analysis

Issue - State: open - Opened by CharlotteAnne about 1 year ago
Labels: enhancement

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

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

#103 - remove all samtools stats

Issue - State: open - Opened by CharlotteAnne about 1 year ago

#101 - Update peak caller documentation

Pull Request - State: open - Opened by vecerkovakaterina over 1 year ago

#100 - Update peak caller documentation

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

#99 - alternative motifs to peka (homer,streme)

Issue - State: open - Opened by CharlotteAnne over 1 year ago

#98 - option to run icount metagene on peaks

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

#97 - paraclu nucleotide position error

Issue - State: open - Opened by CharlotteAnne over 1 year ago - 1 comment
Labels: bug

#96 - allow control input to pureclip

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

#95 - demultiplexing

Issue - State: open - Opened by CharlotteAnne over 1 year ago

#94 - group analysis

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

#93 - 2.0 peaks arent called in test full small

Issue - State: open - Opened by CharlotteAnne over 1 year ago
Labels: bug

#92 - add clipqc and multiqc to 2.0

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

#91 - documentation for 2.0

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

#90 - make conda test pass for peka module

Issue - State: open - Opened by CharlotteAnne over 1 year ago
Labels: bug

#89 - Hackathon

Pull Request - State: closed - Opened by CharlotteAnne over 1 year ago

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

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

#87 - change smrna to ncrna for pre-mapping fa

Issue - State: closed - Opened by iraiosub over 1 year ago - 3 comments
Labels: enhancement

#86 - Feat peakcalling logic

Pull Request - State: closed - Opened by amchakra over 1 year ago

#85 - Convert "target" to "genome"

Issue - State: closed - Opened by amchakra over 1 year ago - 1 comment
Labels: enhancement

#84 - Feat peakcalling modules

Pull Request - State: closed - Opened by iraiosub over 1 year ago

#82 - peak calling subworkflow

Issue - State: open - Opened by CharlotteAnne over 1 year ago

#81 - support for eclip paired end reads

Issue - State: closed - Opened by CharlotteAnne over 1 year ago - 3 comments

#78 - MODULE: pureclip

Issue - State: open - Opened by CharlotteAnne over 1 year ago - 1 comment

#77 - MODULE: peka

Issue - State: closed - Opened by CharlotteAnne over 1 year ago

#76 - MODULE: iCount metagene

Issue - State: closed - Opened by CharlotteAnne over 1 year ago

#75 - Updates

Pull Request - State: open - Opened by chris-cheshire over 1 year ago - 2 comments

#74 - Update main.nf

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

#73 - STAR binary on the container does not work with singularity

Issue - State: closed - Opened by tbrittoborges over 1 year ago - 1 comment
Labels: bug

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

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

#71 - Conda env fails to create

Issue - State: open - Opened by JohnRachid over 1 year ago
Labels: bug

#70 - update aws paths

Pull Request - State: closed - Opened by FriederikeHanssen over 1 year ago - 2 comments

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

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 1 comment

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

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 1 comment

#67 - Process `get_software_versions` terminated with an error exit status （1）

Issue - State: open - Opened by gl9797 about 2 years ago
Labels: bug

#66 - Important! Template update for nf-core/tools v2.6

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 1 comment

#65 - Important! Template update for nf-core/tools v2.5.1

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 1 comment

#64 - Important! Template update for nf-core/tools v2.5

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 1 comment

#63 - Add mimetype to input parameter in schema

Pull Request - State: closed - Opened by drpatelh over 2 years ago

#62 - Important! Template update for nf-core/tools v2.4

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#61 - Important! Template update for nf-core/tools v2.3.2

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#60 - Important! Template update for nf-core/tools v2.3.1

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#59 - Important! Template update for nf-core/tools v2.3

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

#58 - Important! Template update for nf-core/tools v2.2

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 1 comment

#57 - Reads with / characters in the read names cause the pipeline to fail

Issue - State: open - Opened by marc-jones about 3 years ago - 1 comment
Labels: bug

#56 - Dedup and cutadapt fixes

Pull Request - State: closed - Opened by amchakra about 3 years ago

#55 - Important! Template update for nf-core/tools v2.1

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago - 1 comment

#54 - Important! Template update for nf-core/tools v2.0.1

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago - 1 comment

#53 - Important! Template update for nf-core/tools v2.0

Pull Request - State: closed - Opened by KevinMenden over 3 years ago - 1 comment

#52 - Phil fixes

Pull Request - State: closed - Opened by ewels over 3 years ago - 1 comment

#51 - Important! Template update for nf-core/tools v1.14

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago

#50 - Update README.md

Pull Request - State: closed - Opened by drpatelh over 3 years ago - 3 comments

#49 - Add figures to output docs

Issue - State: open - Opened by amchakra over 3 years ago
Labels: documentation

#48 - Minor pre-release updates

Pull Request - State: closed - Opened by drpatelh over 3 years ago - 1 comment

#47 - Pipeline has no release, but not WIP or UNDER CONSTRUCTION warning

Issue - State: closed - Opened by maxulysse over 3 years ago
Labels: bug

#46 - First release

Pull Request - State: closed - Opened by amchakra over 3 years ago - 1 comment

#45 - Feat aws

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

#44 - include details of smRNA mapping

Pull Request - State: closed - Opened by CharlotteAnne over 3 years ago

#43 - Merge #41 into dev

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

#42 - Get tests passing after template merge

Pull Request - State: closed - Opened by drpatelh over 3 years ago - 1 comment

#41 - Added optional process to move UMI to FastQ header

Pull Request - State: closed - Opened by amchakra over 3 years ago

#40 - Nobby edits

Pull Request - State: closed - Opened by amchakra over 3 years ago

#39 - Important! Template update for nf-core/tools v1.13.3

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago

#38 - Important! Template update for nf-core/tools v1.13.2

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago - 1 comment

#37 - Important! Template update for nf-core/tools v1.13.1

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago - 1 comment

#36 - Char edits

Pull Request - State: closed - Opened by charlotte-west over 3 years ago

#35 - Important! Template update for nf-core/tools v1.13

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago - 1 comment

#34 - Peak logic change

Pull Request - State: closed - Opened by charlotte-west over 3 years ago

#33 - CLIPSEQ: Migrate all usage parameters for JSON Schema

Issue - State: closed - Opened by apeltzer over 3 years ago
Labels: enhancement

#32 - initiate new branch

Pull Request - State: closed - Opened by charlotte-west over 3 years ago

#31 - MPI error but it should be running locally

Issue - State: closed - Opened by adomingues over 3 years ago - 11 comments
Labels: bug

#30 - Updates to PureCLIP, motif calling and iCount tmp dir

Pull Request - State: closed - Opened by amchakra over 3 years ago

#29 - iGenomes path is not correct

Issue - State: closed - Opened by adomingues over 3 years ago - 3 comments
Labels: bug

#28 - Pr review

Pull Request - State: closed - Opened by charlotte-west almost 4 years ago

#27 - Updated output docs

Pull Request - State: closed - Opened by amchakra almost 4 years ago

#26 - PSEUDO PR - DO NOT MERGE

Pull Request - State: closed - Opened by ewels almost 4 years ago - 3 comments

#25 - Pseudo PR for first stable release

Pull Request - State: closed - Opened by charlotte-west almost 4 years ago

#24 - PR3 update software versions (regex needs to be checked)

Pull Request - State: closed - Opened by charlotte-west almost 4 years ago

#23 - PR2 Usage docs

Pull Request - State: closed - Opened by charlotte-west almost 4 years ago

#22 - PR1 - cleanup + linting jason schema

Pull Request - State: closed - Opened by charlotte-west almost 4 years ago

#21 - Usage docs

Pull Request - State: closed - Opened by charlotte-west almost 4 years ago

#20 - flag for saving star index

Pull Request - State: closed - Opened by charlotte-west almost 4 years ago

#19 - add smrna organism options

Pull Request - State: closed - Opened by charlotte-west almost 4 years ago

#18 - Feat email

Pull Request - State: closed - Opened by charlotte-west almost 4 years ago

#17 - Feat multiqc

Pull Request - State: closed - Opened by amchakra almost 4 years ago

#16 - Gtf check

Pull Request - State: closed - Opened by charlotte-west almost 4 years ago

#15 - Feat RSeQC

Pull Request - State: closed - Opened by amchakra almost 4 years ago

#14 - Update environment.yml

Pull Request - State: closed - Opened by amchakra almost 4 years ago

#13 - Feat multiqc

Pull Request - State: closed - Opened by amchakra almost 4 years ago
Labels: enhancement

#12 - Feat multiqc

Pull Request - State: closed - Opened by amchakra almost 4 years ago
Labels: enhancement

#11 - Feat software versions

Pull Request - State: closed - Opened by charlotte-west almost 4 years ago