nf-core/demultiplex issues and pull requests

#152 - FEAT: update bclconvert to 4.2.4

Pull Request - State: closed - Opened by maxulysse 8 months ago - 3 comments

#151 - FEAT: update bclconvert to 4.2.4

Pull Request - State: closed - Opened by maxulysse 8 months ago - 2 comments

#150 - [Question]: Upgrading bcl-convert to 4.2.4

Issue - State: open - Opened by tamuanand 8 months ago - 2 comments

#149 - Add samplesheet generation

Issue - State: open - Opened by Emiller88 8 months ago

#148 - Use teams in CODEOWNERS

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

#147 - Add Kraken2 step

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

#146 - Update the citation tools

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

#145 - Fix MultiQC report generation

Pull Request - State: closed - Opened by Aratz 9 months ago - 1 comment

#144 - MultiQC report is empty

Issue - State: open - Opened by Aratz 9 months ago - 1 comment
Labels: bug

#143 - Add option to run CheckQC after demultiplexing with bcl2fastq

Issue - State: open - Opened by matrulda 9 months ago - 2 comments
Labels: enhancement

#142 - Demux dies for empty files

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

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

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

#140 - Make it possible to skip MultiQC

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

#139 - Update samplesheet in usage

Issue - State: open - Opened by Emiller88 11 months ago

#138 - Support different input schema's for different demultiplexers

Issue - State: open - Opened by Emiller88 11 months ago - 1 comment
Labels: enhancement

#137 - Wrong REGEX to exclude "Undetermined" fastq files

Issue - State: closed - Opened by mblohmer 11 months ago
Labels: bug

#135 - Fastq files missing from output / report, 10x single cell

Issue - State: open - Opened by rifius 11 months ago - 2 comments
Labels: bug

#133 - Remove confusing language for sample sheets (related to Issue #98)

Pull Request - State: open - Opened by AdrijaK 12 months ago - 3 comments

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

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

#131 - Bump b2fq tests

Pull Request - State: open - Opened by Emiller88 about 1 year ago - 1 comment

#130 - Remove_aws_ecr_public_profile

Pull Request - State: closed - Opened by adamrtalbot about 1 year ago - 1 comment

#129 - Fix/ci nf tests & Remove un-necessary registry declarations

Pull Request - State: closed - Opened by sateeshperi about 1 year ago - 1 comment
Labels: Ready to review

#128 - Remove un-necessary registry declarations

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 6 comments

#127 - Add singularity.registry = 'quay.io' and bump NF version to 23.04.0

Pull Request - State: closed - Opened by drpatelh about 1 year ago - 1 comment

#126 - Dev -> Master for 1.3.2 release

Pull Request - State: closed - Opened by drpatelh about 1 year ago - 1 comment

#125 - Move containers for pipeline to quay.io

Pull Request - State: closed - Opened by drpatelh about 1 year ago - 1 comment

#124 - Dev -> Master for 1.3.1 patch release

Pull Request - State: closed - Opened by drpatelh about 1 year ago - 1 comment

#123 - Move test data from pipeline to testdatasets

Pull Request - State: closed - Opened by drpatelh about 1 year ago - 1 comment

#122 - Use Nextflow.error instead of 'exit 1'

Pull Request - State: closed - Opened by adamrtalbot about 1 year ago - 3 comments

#121 - Use github URL for Illumina format SampleSheet so -profile test works remotely

Pull Request - State: closed - Opened by adamrtalbot about 1 year ago - 3 comments

#120 - Update docs for v1.3.0 release

Pull Request - State: closed - Opened by adamrtalbot about 1 year ago - 2 comments

#119 - Re-add aws_tower config for running on Tower

Pull Request - State: closed - Opened by adamrtalbot about 1 year ago - 1 comment

#118 - Release candidate 1.3.0

Pull Request - State: closed - Opened by adamrtalbot about 1 year ago - 1 comment

#117 - Bump fastp

Pull Request - State: closed - Opened by matthdsm about 1 year ago - 4 comments

#116 - Ambiguous sampleSheet.csv structure

Issue - State: open - Opened by Gian77 about 1 year ago - 2 comments
Labels: bug

#115 - Update all modules and specify container registry using docker.registry default

Pull Request - State: closed - Opened by adamrtalbot about 1 year ago - 2 comments

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

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago - 2 comments

#113 - CHORES: Back to business as usual

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#112 - Release 1.2.0

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 2 comments

#111 - prepare release: 1.2.0

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 4 comments

#110 - groovify modules/local/csv2tsv.nf

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

#109 - RELEASE: 1.2.0

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 7 comments

#108 - FIX: Move untar to bclconvert and bcl2fastq processes

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 9 comments

#107 - FIX: update test_full with new test data for megatests

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 3 comments

#106 - Input file name collision occurs for fastp and falco

Issue - State: open - Opened by kkami1115 about 1 year ago - 2 comments
Labels: bug

#105 - Regex does not parse sample names correctly

Issue - State: closed - Opened by vitu1 about 1 year ago - 2 comments
Labels: bug

#104 - Fix/update nf tests

Pull Request - State: closed - Opened by sateeshperi about 1 year ago - 1 comment

#103 - -profile test failing due to relative path in flowcell_input.csv

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

#102 - Clean up samplesheet reading

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

#101 - Bump bcl2fastq

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

#100 - Fqtk rebased

Pull Request - State: closed - Opened by sam-white04 over 1 year ago - 2 comments

#99 - Add fqtk as a demultiplexer

Pull Request - State: closed - Opened by sam-white04 over 1 year ago - 3 comments

#98 - Remove confusing samplesheet language

Issue - State: open - Opened by Emiller88 over 1 year ago - 8 comments
Labels: bug

#97 - bcl2fastq installation error

Issue - State: closed - Opened by ushnaahmad over 1 year ago - 10 comments
Labels: bug

#96 - Fix dark image

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

#95 - Codeowners

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

#94 - Update supported sequencing platforms

Pull Request - State: closed - Opened by nh13 over 1 year ago - 1 comment

#93 - Update supported sequencing platforms

Pull Request - State: closed - Opened by nh13 over 1 year ago - 3 comments

#92 - bcl2fastq installation error

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

#91 - Sgdemux dev

Pull Request - State: closed - Opened by sam-white04 over 1 year ago - 6 comments

#90 - Documentation and file type for SampleSheet.csv

Issue - State: open - Opened by mschubert over 1 year ago - 3 comments
Labels: enhancement

#89 - Logo on the readme is broken

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

#88 - Add code-owners

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

#87 - For sample demultiplexing from FASTQs, add fqtk.

Issue - State: open - Opened by Emiller88 over 1 year ago - 8 comments
Labels: enhancement

#86 - Dev -> Master for 1.1.0 release

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

#85 - Prepare for 1.1.0 release

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

#84 - skip_tools comment says list, schema says string

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

#83 - fixed if statements for skip_tools

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

#82 - Optional fastp and falco skip statements seem to be incorrect

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

#81 - What is the status of the test_full?

Issue - State: open - Opened by maxulysse over 1 year ago - 4 comments
Labels: enhancement

#80 - The process stop or cannot find correct file path when add NoLaneSplitting, true

Issue - State: closed - Opened by wzheng0520 over 1 year ago - 3 comments
Labels: bug

#79 - It looks like samplesheet.csv doesn't exist.

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

#78 - 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

#77 - 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

#76 - Highlight test files

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

#75 - Feat/update input parsing

Pull Request - State: closed - Opened by matthdsm over 1 year ago - 6 comments

#74 - Test Groovy Functions

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

#73 - nf-test init

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

#72 - Migrate to nf-test

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

#70 - Feat/wf qc options

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

#69 - Make running `falco` optional

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

#68 - Make trimming optional

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

#67 - Enable instititutional configs

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

#66 - add subway map

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

#65 - add subway map

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

#64 - MultiQC report is empty

Issue - State: open - Opened by matthdsm over 1 year ago - 4 comments
Labels: bug

#63 - Workflow updates

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

#62 - Replace `fastqc` with `falco`

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

#61 - Dev -> Master for 1.0.0 release

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

#60 - RFC: Convert to stand-alone subworkflow(s)

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

#59 - Add support for `WatchPath`

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

#58 - Release prep

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

#57 - Allow bases2fastq to handle trimming by default

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

#56 - bases2fastq doesn't use generate_fastq_meta so fcid is null

Issue - State: closed - Opened by Emiller88 over 1 year ago - 2 comments
Labels: bug

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

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

#54 - Add output dir back to bases2fastq

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

#53 - Create a bases2fastq MultiQC Module

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

#52 - Remove subworkflows/local/input_check.nf

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

#51 - Bases2fastq

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

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

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

GitHub / nf-core/demultiplex issues and pull requests