Ecosyste.ms: Issues

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GitHub / nf-core/ampliseq issues and pull requests

#554 - Let QIIME2 accept special symbols in taxonomy strings

Pull Request - State: closed - Opened by d4straub over 1 year ago - 2 comments

#553 - Fix empty barrnap output

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

#552 - Ampliseq fails during reannotation of ASVs

Issue - State: closed - Opened by pragermh over 1 year ago - 9 comments
Labels: bug

#551 - Update version to 2.6.0dev

Pull Request - State: closed - Opened by d4straub over 1 year ago - 6 comments

#550 - Review suggestions

Pull Request - State: closed - Opened by d4straub over 1 year ago - 2 comments

#549 - Release 2.5.0

Pull Request - State: closed - Opened by d4straub over 1 year ago - 5 comments

#548 - change barrnap filtering

Pull Request - State: closed - Opened by d4straub over 1 year ago - 1 comment

#547 - ASV filtering with barrnap could be improved

Issue - State: closed - Opened by d4straub over 1 year ago - 2 comments
Labels: enhancement

#546 - Prepare for release 2.4.2

Pull Request - State: closed - Opened by d4straub over 1 year ago - 1 comment

#545 - Fix addsh

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

#544 - Fix fasta input

Pull Request - State: closed - Opened by jtangrot over 1 year ago - 15 comments

#543 - bin/add_sh_to_taxonomy.py needs updating to match UNITE db files

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

#542 - Strange results with fasta input

Issue - State: closed - Opened by jtangrot almost 2 years ago - 9 comments
Labels: bug

#541 - Remove taxonomic adjustments

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

#540 - module compilation error

Issue - State: closed - Opened by skose82 almost 2 years ago - 7 comments
Labels: bug

#539 - COI accepted for SBDIexport

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

#538 - Sample filter

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

#537 - Fix sbdi export

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

#536 - Samples with '-' in name get converted to '.' after dada2 steps

Issue - State: closed - Opened by davised almost 2 years ago - 13 comments
Labels: bug

#535 - Run barrnap with fasta

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

#534 - Add COIDB documentation

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

#533 - Barrnap doesn't get called with fasta input

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

#532 - Pipeline finishes with no plots/analysis with qiime2

Issue - State: closed - Opened by skose82 almost 2 years ago - 2 comments
Labels: bug

#531 - Update metadata documentation

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

#530 - Fix conda packages

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

#529 - fix black formatting

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

#528 - Update QIIME2 from 2022.8 to 2022.11

Pull Request - State: closed - Opened by d4straub almost 2 years ago - 4 comments

#527 - Output format cannot be FASTQ since no quality values are available

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

#526 - Run exits with exit status (137) even when --max_memory specified

Issue - State: closed - Opened by srikanthkris almost 2 years ago - 6 comments

#525 - Filter samples by total counts before downstream analysis

Issue - State: closed - Opened by d4straub almost 2 years ago - 1 comment
Labels: enhancement

#524 - Error when running the pipeline on a machine with Apple silicon (M1 processor)

Issue - State: closed - Opened by gbaiao almost 2 years ago - 6 comments

#523 - Parallelization processes in DADA2_DENOISE and RM_CHIMERAS

Issue - State: closed - Opened by sgaleraalq almost 2 years ago - 9 comments
Labels: enhancement

#522 - Bug with v2.4.1: categorical data required in metadata

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

#521 - export DADA2 QC svg

Pull Request - State: closed - Opened by d4straub almost 2 years ago - 1 comment

#520 - add conda package digest

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

#519 - Pipeline reference to multiqc report

Pull Request - State: closed - Opened by d4straub almost 2 years ago - 1 comment

#518 - Add COIDB DADA2 reference taxonomy database

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

#517 - no space left on device error

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

#516 - QIIME2_DIVERSITY: QIIME2_TREE Not working for me

Issue - State: closed - Opened by sgaleraalq almost 2 years ago - 33 comments
Labels: bug

#515 - Cannot specify version of GTDB in ampliseq v2.3.1

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

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

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

#513 - Merging template updates 2.7.2

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

#511 - Adding the pipeline reference to the MultiQC report

Issue - State: closed - Opened by d4straub almost 2 years ago - 1 comment
Labels: enhancement

#510 - 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

#509 - Bump version to 2.5.0dev

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

#508 - replace single backslashes with double backslashes

Pull Request - State: closed - Opened by d4straub almost 2 years ago - 1 comment

#507 - Apply review suggestions

Pull Request - State: closed - Opened by d4straub almost 2 years ago - 1 comment

#506 - Release 2.4.1

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

#505 - change version to 2.4.1

Pull Request - State: closed - Opened by d4straub almost 2 years ago - 1 comment

#503 - fix FORMAT_TAXONOMY_QIIME

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

#472 - Add GBIF adapted CO1 database

Issue - State: closed - Opened by erikrikarddaniel about 2 years ago - 16 comments
Labels: enhancement

#471 - Add VSEARCH/SINTAX taxonomy annotation

Issue - State: closed - Opened by erikrikarddaniel about 2 years ago - 4 comments
Labels: enhancement, documentation

#450 - Implement translation filtering for protein coding markers

Issue - State: closed - Opened by tjcreedy over 2 years ago - 6 comments
Labels: enhancement

#436 - Adapt ampliseq SBDI output format to changes in ASV portal

Issue - State: closed - Opened by pragermh over 2 years ago - 6 comments

#236 - Phylogenetic placement of ASVs

Issue - State: closed - Opened by erikrikarddaniel over 3 years ago - 5 comments
Labels: enhancement

#64 - Add demultiplexing step

Issue - State: open - Opened by DiegoBrambilla almost 6 years ago - 7 comments
Labels: enhancement