Ecosyste.ms: Issues

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GitHub / nf-core/dualrnaseq issues and pull requests

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

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

#92 - update unzip files

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

#91 - Feature/count reads

Pull Request - State: open - Opened by mauro-saporita about 1 year ago

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

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

#88 - Are there plans to port the workflow to DSL2?

Issue - State: open - Opened by scontente over 1 year ago - 2 comments

#87 - Refactoring uncompress

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

#86 - Tximport hots module

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

#85 - add test data for loading 2 genome.fasta files, and modify PREPARE_x_TRANSCRIPTOME modules

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

#84 - Refactoring uncompress

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

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

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

#82 - emit extracted annotations

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

#81 - fix prepare_reference_files subworkflow

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

#79 - fix Salmon SA subworkflow

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

#78 - Added a draft of HTSEQ module and STAR_HTSEQ subworkflow

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

#77 - initial commit for replace data

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

#76 - Extract processed reads

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

#75 - Create STAR_HTSEQ subworkflow + HTSEQ module

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

#74 - Convert all replace modules in PREPARE_REFERENCE_DATA

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

#73 - rethink check_replicates process for DSL2

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

#72 - Extract annotations

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

#71 - 56-fix subworkflow after adding trna

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

#69 - Add module extract processed reads to the pipeline

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

#68 - add small host trna gff file to test dataset

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

#67 - Salmon quantification

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

#66 - Add a module for count_total_reads and count_total_read_pairs processes

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

#65 - 56 create transcriptiome workflow

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

#64 - create a module for generating bacterial transcriptome fasta file

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

#63 - fix #58

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

#62 - Add salmon quantification to salmon_alignment_base subworkflow

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

#61 - Feature/salmon split table

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

#60 - Update salmon split table process to DSL2

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

#59 - Star modules

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

#58 - salmon quantification is not executed for all samples

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

#57 - Combine host annotations with quantification results

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

#56 - Create subworkflow to create combined host/path transcriptome file

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

#55 - add updated test hackathon dataset

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

#54 - Update extract_annotations_* to DSL2

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

#53 - Update star indexing and star alignment processes from DSL1 processes to DSL2 modules

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

#52 - use samples spreadsheet from test-dataset repository

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

#51 - Dual 46

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

#50 - Feature/cutadapt

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

#49 - Dualrnaseq 45 update salmon

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

#48 - A new module to combine the host ambig and unique counts

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

#47 - add test data set for hackathon

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

#46 - Create COMBINE_QUANTIFICATION_RESULTS modules

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

#45 - Update salmon index and salmon quantification process from DSL1 process to DSL2 module

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

#44 - Update tximport_host process from DSL1 process to DSL2 module

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

#43 - Update Cutadapt process to DSL2

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

#42 - create test dataset for DSL2 pipeline

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

#41 - create a base for transition to DSL2

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

#40 - update aws paths

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

#38 - 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

#37 - 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

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

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

#35 - 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

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

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

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

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

#32 - 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

#31 - 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

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

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

#29 - on scatterplots, allow seaborn 0.11.2 to also put Pearson's r on the …

Pull Request - State: open - Opened by rafalcode almost 3 years ago - 2 comments

#28 - seaborn version incompats.

Issue - State: open - Opened by rafalcode almost 3 years ago
Labels: enhancement

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

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

#26 - Parsing multiple gff features not working

Issue - State: closed - Opened by gprezza almost 3 years ago - 1 comment

#25 - feature names hardcoded in extract_annotations_from_gff.py

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

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

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

#23 - Workflow does not start due to error

Issue - State: closed - Opened by rcostan00b over 3 years ago - 6 comments
Labels: bug

#22 - 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

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

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

#20 - Updating parameters schema and readme

Pull Request - State: open - Opened by reganhayward over 3 years ago - 1 comment

#19 - Remove `parameters.md`

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

#18 - Switch to use standard nf-core iGenomes config

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

#17 - Output separate coverage files for host and pathogen

Issue - State: open - Opened by gprezza over 3 years ago - 1 comment
Labels: enhancement

#16 - Template 1.14 update

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

#15 - Template update for nf-core/tools version 1.14

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

#14 - Pipeline needs updating to the latest template version

Issue - State: open - Opened by ewels over 3 years ago
Labels: enhancement

#13 - `TEMPLATE` branch is dirty

Issue - State: closed - Opened by ewels over 3 years ago - 2 comments
Labels: bug

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

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

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

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

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

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

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

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

#8 - Zenodo DOI Addition

Issue - State: closed - Opened by apeltzer almost 4 years ago - 1 comment
Labels: enhancement

#7 - updated dev version

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

#6 - DEV -> MASTER Release PR for initial release

Pull Request - State: closed - Opened by bozmik almost 4 years ago - 5 comments

#5 - DO NOT MERGE - Pseudo PR - community review for initial release

Pull Request - State: closed - Opened by maxulysse almost 4 years ago - 2 comments

#4 - Revert "Pseudo PR - community review for initial release"

Pull Request - State: closed - Opened by maxulysse almost 4 years ago - 1 comment

#3 - Pseudo PR - community review for initial release

Pull Request - State: closed - Opened by ewels almost 4 years ago - 2 comments

#2 - Important! Template update for nf-core/tools v1.12.1

Pull Request - State: closed - Opened by nf-core-bot almost 4 years ago

#1 - Important! Template update for nf-core/tools v1.12

Pull Request - State: closed - Opened by nf-core-bot about 4 years ago