nf-core/nascent issues and pull requests

#124 - Saving BWA MEM log

Issue - State: open - Opened by Caffeinated-Code 9 months ago
Labels: enhancement

#123 - Discrepancy between bigwigs generated by bedtools and deeptools

Issue - State: open - Opened by Caffeinated-Code 9 months ago
Labels: bug

#122 - Scatter ci

Pull Request - State: open - Opened by Emiller88 9 months ago - 1 comment

#121 - Test results say chr22 when the ref is chr21?

Issue - State: open - Opened by Emiller88 9 months ago
Labels: bug

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

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

#119 - Issues of creating BWA index with custom fasta and GTF

Issue - State: open - Opened by YoshikiHigashijima 10 months ago
Labels: bug

#118 - Which assay type (GRO-seq, PRO-seq ... etc) should I use for EU-seq?

Issue - State: open - Opened by YoshikiHigashijima 10 months ago
Labels: enhancement

#117 - Use fromSamplesheet

Pull Request - State: closed - Opened by Emiller88 11 months ago - 1 comment

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

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

#115 - Flipped bigwig strands in PROseq samples

Issue - State: open - Opened by Caffeinated-Code about 1 year ago - 2 comments
Labels: bug

#114 - Add in nf-validation for samplesheet

Issue - State: open - Opened by Emiller88 about 1 year ago - 2 comments
Labels: enhancement

#113 - "ERROR ~ fromIndex = -1" during samtools sort step

Issue - State: closed - Opened by andreagillespie about 1 year ago - 6 comments
Labels: bug

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

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

#111 - refactor(#107): Clean up Multiqc mix

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

#110 - Dev -> Master for 2.1.1 release

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

#109 - Fix index lacking a meta map causing igenomes and premade indexes to fail

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

#108 - test_full profile is broken

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

#107 - Clean up Multiqc channels

Issue - State: closed - Opened by Emiller88 over 1 year ago

#106 - Error executing process > 'NFCORE_NASCENT:NASCENT:ALIGN_BWA:BWA_MEM (1)'

Issue - State: closed - Opened by MathewBerg9 over 1 year ago
Labels: bug

#105 - BEDTOOLS_INTERSECT_FILTER is not invoked before accessing the output attribute in release version

Issue - State: closed - Opened by jianhong over 1 year ago - 3 comments
Labels: bug

#104 - Dev -> Master for 2.1.0 release

Pull Request - State: closed - Opened by Emiller88 over 1 year ago - 3 comments

#103 - Release prep

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

#102 - Bedtools sort output isn't deterministic

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: bug

#101 - nf-test

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

#100 - Docs cleanup

Pull Request - State: closed - Opened by Emiller88 over 1 year ago - 2 comments

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

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

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

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

#97 - Missing homer outputs

Pull Request - State: closed - Opened by Emiller88 over 1 year ago - 1 comment
Labels: bug

#96 - Obligatory metro map

Pull Request - State: open - Opened by Emiller88 over 1 year ago - 8 comments

#95 - Improve reporting when no transcripts are found

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: enhancement

#94 - Filter and intersect

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

#93 - Example of 3D genome integration

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: enhancement

#92 - motif production for region

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: enhancement

#91 - Example of integration with ATAC-seq pipeline output

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: enhancement

#90 - Support STAR

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: enhancement

#89 - Clean up published files

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: enhancement

#88 - Add plotHeatmap by Gene and by Transcript

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: enhancement

#87 - Fixed DOI with correct URL

Pull Request - State: closed - Opened by apeltzer over 1 year ago - 3 comments

#86 - Post release chores

Pull Request - State: closed - Opened by Emiller88 over 1 year ago

#85 - Refactor ext.when

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: enhancement

#84 - Migrate CI tests to pytest-workflow

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: enhancement

#83 - dev -> Master for 2.0.0 release

Pull Request - State: closed - Opened by Emiller88 over 1 year ago - 2 comments

#82 - Release prep

Pull Request - State: closed - Opened by Emiller88 over 1 year ago - 2 comments

#81 - Cleanup style

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

#80 - Docs

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

#79 - fix(featurecounts): Update multiqc config to include featurecounts

Pull Request - State: closed - Opened by Emiller88 over 1 year ago - 4 comments

#78 - Set up AWS Full tests

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: enhancement

#77 - Add dedup

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

#76 - Adapter trimming

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

#75 - nf-core subworkflows install

Pull Request - State: closed - Opened by Emiller88 over 1 year ago - 2 comments

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

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

#73 - Include Homer annotate peaks from chip-seq

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

#72 - Add PINTS Visualizer

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

#71 - Investigate adapter trimming

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

#70 - Pass CI

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

#69 - Update Introduction (Pipeline Summary)

Pull Request - State: closed - Opened by sruthipsuresh almost 2 years ago - 1 comment

#68 - Create Subway pipeline

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

#67 - Optimize grohmm parameter tuning and transcript calling

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

#66 - Add full test dataset

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

#65 - Grohmm tuning

Pull Request - State: closed - Opened by Emiller88 almost 2 years ago - 1 comment
Labels: bug

#64 - Add CHM13 igenomes reference

Pull Request - State: closed - Opened by Emiller88 almost 2 years ago - 7 comments

#63 - Document grohmm Tuning

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

#62 - Update Documentation

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

#61 - Pass All CI

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

#60 - Refactor Prepare Genome

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

#59 - Dragmap

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

#58 - Pints

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

#57 - Add homer uniqmap creation

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

#56 - GROHMM and CHM13

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

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

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

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

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

#53 - Fix grouping

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

#52 - Small testdata

Pull Request - State: closed - Opened by Emiller88 almost 2 years ago - 1 comment
Labels: bug

#51 - Use smaller GRCh38 BWA index for tests

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

#50 - Merge featurecounts

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

#49 - Featurecounts only counts Exons

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

#48 - Add dynseq tracks

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

#47 - Added Keep Standard Chromosomes function to standardize bam file and address error

Pull Request - State: closed - Opened by Emiller88 about 2 years ago
Labels: bug

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

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

#45 - style: Run formatters

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

#44 - Upstream Subworkflows

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

#43 - Fix CI

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

#42 - Update bbmap path

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

#41 - Support and benchmark aligners

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

#40 - Upstream modules

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

#39 - Support both NT and TSS assays

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

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

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

#37 - 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

#36 - fix(multiqc): Remove GROHMM output which may not be there

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

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

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

#34 - Find citations for software

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

#33 - Fix GroHMM on full runs

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

#32 - Create dREG container

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

#31 - Test with dREG web submission

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

#30 - Add IGV tools

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

#29 - Update local module tests

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

#28 - Add dragmap

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

#27 - Upstream Module Changes

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

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

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

#25 - Manual Template update

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

GitHub / nf-core/nascent issues and pull requests