Ecosyste.ms: Issues

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GitHub / nf-core/mag issues and pull requests

#432 - Replace hardocded URL with paramater

Pull Request - State: closed - Opened by jfy133 almost 2 years ago - 1 comment

#431 - Entry point to pipeline at binning stage

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

#430 - How to fix the working environment when running the nf-core/mag pipeline?

Issue - State: closed - Opened by rbguevarra5 almost 2 years ago - 2 comments
Labels: bug

#429 - Spades assembly failed with the error code 250

Issue - State: closed - Opened by mathavanpu almost 2 years ago - 3 comments
Labels: bug

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

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 4 comments

#427 - Fix missing html tag and ToC in output docsfor BBnorm section

Pull Request - State: closed - Opened by jfy133 almost 2 years ago - 2 comments

#426 - Fix typo in parameter help text (`--host_genome` and `--host_fasta`)

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

#425 - Feature can added to the MAG pipeline

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

#424 - Error executing process > 'NFCORE_MAG:MAG:GTDBTK:GTDBTK_DB_PREPARATION (gtdbtk_r202_data.tar.gz)'

Issue - State: closed - Opened by johnne almost 2 years ago - 8 comments
Labels: bug

#423 - Error executing CONCOCT: Process exceeded running time limit (4h)

Issue - State: closed - Opened by mlbonatelli almost 2 years ago - 5 comments
Labels: bug

#422 - Digital normalization with BBnorm

Pull Request - State: closed - Opened by erikrikarddaniel almost 2 years ago - 11 comments

#421 - samplesheet - does not recognize path information

Issue - State: closed - Opened by kullrich almost 2 years ago - 1 comment
Labels: bug

#420 - Test - not running

Issue - State: closed - Opened by kullrich almost 2 years ago - 3 comments
Labels: bug

#419 - Fix busco_clean parameter being enabled by default

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

#418 - Error with BOWTIE2_ASSEMBLY_ALIGN

Issue - State: open - Opened by bmlab-sg almost 2 years ago - 1 comment
Labels: bug

#417 - Issue with MAG_DEPTHS_PLOT

Issue - State: open - Opened by x-rv almost 2 years ago - 3 comments

#416 - Update to GTDBTK_CLASSIFYWF nf-core module

Pull Request - State: closed - Opened by alxndrdiaz almost 2 years ago - 2 comments
Labels: enhancement, ready to review

#415 - Test data samplesheet is using old S3 paths

Issue - State: closed - Opened by Lfulcrum almost 2 years ago - 4 comments
Labels: bug

#414 - Hardcoded url in main workflow

Issue - State: closed - Opened by erikrikarddaniel almost 2 years ago - 1 comment
Labels: bug

#413 - Add dereplication with dRep

Issue - State: open - Opened by erikrikarddaniel almost 2 years ago - 4 comments
Labels: enhancement

#412 - Add digital normalization

Issue - State: closed - Opened by erikrikarddaniel almost 2 years ago - 3 comments
Labels: enhancement

#411 - Update description of additional Bowtie2 and SPAdes parameters used in command line

Issue - State: closed - Opened by skrakau almost 2 years ago
Labels: enhancement, good first issue

#410 - Update MultiQC report

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

#409 - Update local GTDB-Tk module to newest nf-core module

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

#408 - Bug in mag/subworkflows/local/checkm_qc.nf

Issue - State: closed - Opened by kibet-gilbert almost 2 years ago - 4 comments
Labels: bug

#407 - New test data paths

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

#406 - Fix CheckM db always being downloaded

Pull Request - State: closed - Opened by jfy133 almost 2 years ago - 1 comment

#405 - Downloading of CheckM database always occurs even CheckM not requested

Issue - State: closed - Opened by jfy133 almost 2 years ago
Labels: bug

#403 - Deactivate CONCOCT binning from full tests

Issue - State: closed - Opened by jfy133 almost 2 years ago - 5 comments
Labels: bug

#402 - remove BUSCO warning from stdout log

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

#395 - Add domain-level classification for bins

Pull Request - State: closed - Opened by prototaxites almost 2 years ago - 13 comments

#393 - Move BUSCO.nf process to a bash script

Issue - State: closed - Opened by jfy133 almost 2 years ago
Labels: enhancement, low-priority

#390 - NFCORE_MAG:MAG:PROKKA (SPAdes-DASToolUnbinned-SRR4420310)` terminated with an error exit status (2)

Issue - State: closed - Opened by rialc13 about 2 years ago - 4 comments
Labels: bug

#389 - NFCORE_MAG:MAG:SPADES (SRR9680483)` terminated with an error exit status (245)

Issue - State: closed - Opened by rialc13 about 2 years ago - 6 comments
Labels: bug

#388 - Bin eukaryotic contigs separately using contig classifier

Issue - State: closed - Opened by prototaxites about 2 years ago - 5 comments
Labels: enhancement

#383 - MAG_DEPTHS_PLOT issue

Issue - State: open - Opened by Vikash84 about 2 years ago - 6 comments
Labels: bug

#381 - Evaluate removal of host reads with Bowtie2

Issue - State: open - Opened by skrakau about 2 years ago - 1 comment
Labels: enhancement

#379 - define the SPADES options and GTDB path

Issue - State: closed - Opened by juejun14 about 2 years ago - 6 comments
Labels: enhancement

#375 - From where is gtdbtk_summary getting the qc_discarded_bins information

Issue - State: open - Opened by rialc13 about 2 years ago - 2 comments

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

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

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

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

#364 - Added geNomad tool for viral classification of assemblies

Pull Request - State: closed - Opened by PhilPalmer about 2 years ago - 18 comments

#359 - Add support for single-end reads (in addition to paired-end reads)

Issue - State: open - Opened by alexhbnr about 2 years ago - 8 comments
Labels: enhancement

#358 - Allow to provide multiple FastQs per sample

Issue - State: closed - Opened by alexhbnr about 2 years ago - 3 comments
Labels: enhancement

#354 - Mag with AWS Batch

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

#346 - Add Bakta as alternative to Prokka

Issue - State: open - Opened by jfy133 over 2 years ago - 8 comments
Labels: enhancement, low-priority

#337 - MAG_DEPTHS_PLOT error for `*-binDepths.tsv` files with only one bin

Issue - State: closed - Opened by bbagy over 2 years ago - 9 comments
Labels: bug

#336 - GTDB-TK fails due to insufficient memory

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

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

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

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

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

#311 - Bowtie2 sections broken in MultiQC

Issue - State: closed - Opened by skrakau over 2 years ago - 1 comment
Labels: bug

#310 - update MultiQC report

Pull Request - State: closed - Opened by jfy133 over 2 years ago - 12 comments

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

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

#294 - Including functional profile step

Issue - State: closed - Opened by jacodela almost 3 years ago - 2 comments
Labels: enhancement

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

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

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

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

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

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

#275 - Add separate Nanopore input option

Issue - State: open - Opened by ljmesi almost 3 years ago - 14 comments
Labels: enhancement

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

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

#250 - Digital normalisation

Issue - State: closed - Opened by d4straub over 3 years ago - 1 comment
Labels: enhancement

#238 - Update gtdbtk conda channel

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

#237 - Binnacle for scaffolding of Megahit contigs

Issue - State: closed - Opened by d4straub over 3 years ago - 1 comment
Labels: enhancement

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

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

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

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

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

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

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

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

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

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

#171 - Switch to DSL2

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

#169 - Generalize modules where possible and port to nf-core/modules

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

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

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

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

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

#105 - Update CAT

Issue - State: open - Opened by skrakau over 4 years ago - 1 comment
Labels: enhancement

#40 - pipeline halts when quast finds no min length contigs

Issue - State: closed - Opened by ivelsko almost 5 years ago - 3 comments
Labels: enhancement

#39 - Improvements - Possible merge with YAMP

Issue - State: closed - Opened by HadrienG almost 5 years ago - 1 comment

#37 - Help running in offline cluster

Issue - State: closed - Opened by telatin almost 5 years ago - 4 comments

#34 - Experience from recent assemblies - proposals for improvements

Issue - State: closed - Opened by d4straub about 5 years ago - 1 comment
Labels: enhancement