Ecosyste.ms: Issues

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GitHub / nf-core/bacass issues and pull requests

#116 - 115 add flye to nf corebacass

Pull Request - State: open - Opened by lborcard 7 months ago - 5 comments

#115 - Add flye to nf-core/bacass

Issue - State: open - Opened by lborcard 7 months ago - 5 comments

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

Pull Request - State: open - Opened by nf-core-bot 7 months ago

#113 - URGENT: pin nf-validation version

Issue - State: open - Opened by nvnieuwk 7 months ago - 1 comment
Labels: bug

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

Pull Request - State: closed - Opened by nf-core-bot 7 months ago

#111 - Merge nf-core Template Update v2.12

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

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

Pull Request - State: closed - Opened by nf-core-bot 8 months ago

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

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

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

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

#106 - Revamping Dragonflye: Introducing Hybrid Mode & Patch Updates

Pull Request - State: closed - Opened by Daniel-VM 11 months ago - 9 comments

#105 - Allow dragonflye to polish draft genome with short-reads

Issue - State: closed - Opened by Daniel-VM 11 months ago
Labels: enhancement

#104 - Add module dragonflye for long-reads assembly

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

#103 - update bakta to v1.8.2

Pull Request - State: closed - Opened by Daniel-VM 11 months ago - 2 comments

#102 - Update bakta to v1.8.2

Issue - State: closed - Opened by Daniel-VM 11 months ago
Labels: enhancement

#101 - New module - dragonflye - for long-read assembly

Issue - State: closed - Opened by Daniel-VM 11 months ago
Labels: enhancement

#100 - Bump version 2.2.0dev

Pull Request - State: closed - Opened by Daniel-VM 11 months ago - 2 comments

#99 - Bump version 2.2.0dev

Pull Request - State: closed - Opened by Daniel-VM 11 months ago - 2 comments

#98 - dummy change to update github test #97

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

#97 - Release 2.1.0

Pull Request - State: closed - Opened by Daniel-VM 11 months ago - 7 comments

#96 - Prepare release 2.1.0

Pull Request - State: closed - Opened by Daniel-VM 12 months ago - 10 comments

#95 - Add new module for gene annotation: Bakta

Pull Request - State: closed - Opened by Daniel-VM 12 months ago - 6 comments

#94 - Removal of Prokka in favor of Bakta

Issue - State: closed - Opened by Daniel-VM 12 months ago - 3 comments
Labels: enhancement

#93 - Redirect the module statistics to multiqc

Pull Request - State: closed - Opened by Daniel-VM 12 months ago - 1 comment

#92 - Enhance MultiQC to collect stats from all supported modules

Issue - State: closed - Opened by Daniel-VM about 1 year ago
Labels: enhancement

#91 - Update nf-core template v2.10

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

#90 - Released nf-core v2.10 template

Issue - State: closed - Opened by Daniel-VM about 1 year ago
Labels: enhancement

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

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

#88 - nf-validation on samplesheet

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

#87 - nf-validation on sample sheet

Issue - State: closed - Opened by Daniel-VM about 1 year ago - 3 comments
Labels: enhancement

#86 - Merging template updates 2.9 and workflow update

Pull Request - State: closed - Opened by Daniel-VM about 1 year ago - 13 comments

#85 - Working on updating the nf-core/tools template v2.9

Issue - State: closed - Opened by Daniel-VM about 1 year ago - 2 comments
Labels: enhancement

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

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

#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 - Single end Illumina processing?

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

#81 - 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

#80 - 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

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

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

#78 - skewer.nf problem with Docker container.

Issue - State: open - Opened by mbyott about 2 years ago - 3 comments
Labels: bug

#77 - 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

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

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

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

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

#74 - 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

#73 - 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

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

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

#71 - Regex problem

Issue - State: closed - Opened by tiendu over 2 years ago - 4 comments

#70 - Fixes #69 nanoplot error

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

#69 - Nanoplot expect png output in hybrid assembly mode

Issue - State: open - Opened by jenmuell over 2 years ago
Labels: bug

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

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

#67 - Check for spaces in IDs in Sample Sheet

Issue - State: open - Opened by ThHarbig almost 3 years ago - 1 comment
Labels: enhancement

#66 - Add homopolish for nanopore-only assembly

Issue - State: open - Opened by llk578496 about 3 years ago - 2 comments
Labels: enhancement

#65 - sample sheet check reports wrong row item

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

#64 - samplesheet should have a suffix .tsv if it is a tab-separated file as described

Issue - State: open - Opened by antunderwood about 3 years ago - 7 comments
Labels: bug

#63 - Assembly Polishing is not working in the V2.0

Issue - State: closed - Opened by varunshamanna about 3 years ago - 3 comments
Labels: bug

#62 - bump version to 2.1.0dev

Pull Request - State: closed - Opened by d4straub about 3 years ago - 1 comment

#61 - Local processes to nf-core/modules

Issue - State: open - Opened by d4straub about 3 years ago - 1 comment

#60 - resolve reviewer comments

Pull Request - State: closed - Opened by d4straub about 3 years ago

#59 - Prepare release 2.0.0

Pull Request - State: closed - Opened by d4straub about 3 years ago - 2 comments

#58 - prepare release

Pull Request - State: closed - Opened by d4straub about 3 years ago - 1 comment

#57 - List of ideas to improve assemblies

Issue - State: open - Opened by d4straub about 3 years ago - 9 comments
Labels: enhancement, help wanted, question

#56 - Merging template updates 2.1

Pull Request - State: closed - Opened by d4straub about 3 years ago - 13 comments

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

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

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

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

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

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

#52 - Conversion to DSL2 & update of tools

Issue - State: closed - Opened by d4straub about 3 years ago - 2 comments

#51 - Unicycler version issue

Issue - State: closed - Opened by lch14forever over 3 years ago - 4 comments

#50 - [Question] how to reduce Docker image size

Issue - State: closed - Opened by tamuanand over 3 years ago - 1 comment

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

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

#48 - Remove social preview image to use GitHub OpenGraph

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

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

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

#46 - 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

#45 - Fix broken link

Pull Request - State: closed - Opened by rivera10 over 3 years ago - 1 comment

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

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

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

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

#42 - Documentation broken link

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

#41 - Can we access kraken2db from S3 bucket?

Issue - State: closed - Opened by piroonj over 3 years ago - 4 comments
Labels: question

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

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

#39 - Bugfixes + template

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

#38 - Fix issue #36 regarding kraken2db

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

#37 - Add back tests for kraken

Issue - State: closed - Opened by apeltzer almost 4 years ago - 2 comments

#36 - kraken2db not being mounted for singularity

Issue - State: closed - Opened by santiagorevale almost 4 years ago - 7 comments
Labels: enhancement

#35 - QUAST module not used in MultiQC

Issue - State: closed - Opened by apeltzer almost 4 years ago - 2 comments
Labels: enhancement

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

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

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

Pull Request - State: closed - Opened by nf-core-bot almost 4 years ago - 1 comment

#32 - PR for Maintenance Release 1.1.1

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

#31 - Replace megacontainer with single biocontainers

Issue - State: closed - Opened by apeltzer almost 4 years ago - 2 comments
Labels: enhancement, help wanted

#30 - Fix container profiles, vars in correct scope

Pull Request - State: closed - Opened by Shellfishgene about 4 years ago - 1 comment

#29 - Important! Template update for nf-core/tools v1.10.2

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

#28 - Pilon issue (default_jvm_mem_opts)

Issue - State: open - Opened by xlinxlin about 4 years ago - 8 comments
Labels: enhancement, question

#27 - skewer: command not found with Singularity profile

Issue - State: closed - Opened by ropolomx over 4 years ago - 3 comments
Labels: bug, question

#26 - skip-kraken2 requires Kraken2 DB arg

Issue - State: closed - Opened by ropolomx over 4 years ago - 2 comments
Labels: bug, enhancement

#25 - quast: command not found

Issue - State: closed - Opened by xlinxlin over 4 years ago - 10 comments

#24 - Failed to create conda environment (timeout?)

Issue - State: closed - Opened by xlinxlin over 4 years ago - 2 comments

#23 - Add A5-miseq support

Issue - State: open - Opened by vinisalazar over 4 years ago - 3 comments
Labels: enhancement, help wanted

#22 - Dev

Pull Request - State: closed - Opened by angelovangel over 4 years ago

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

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

#20 - Add social preview image

Pull Request - State: closed - Opened by maxulysse over 4 years ago

#19 - Fix Zenodo DOI in readme

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

#18 - Readme asks users to cite ATAC-seq pipeline

Issue - State: closed - Opened by ewels over 4 years ago - 2 comments
Labels: bug

#17 - tbl2asn is expired

Issue - State: closed - Opened by zdk123 over 4 years ago - 11 comments