Ecosyste.ms: Issues

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GitHub / nf-core/ampliseq issues and pull requests

#653 - I didn't receive an email notification

Issue - State: closed - Opened by luozhy88 about 1 year ago - 3 comments
Labels: bug

#652 - Report shows wrong taxonomic classification stats for QIIME with UNITE

Issue - State: open - Opened by d4straub about 1 year ago - 2 comments
Labels: bug

#651 - Bump version to 2.8.0dev

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

#650 - Requirement Exceeds Available Memory for CUTADAPT

Issue - State: closed - Opened by aqsakhalid03 about 1 year ago - 7 comments
Labels: bug

#649 - CUTADAPT Workflow error

Issue - State: closed - Opened by aqsakhalid03 about 1 year ago - 5 comments
Labels: bug

#648 - Release 2.7.0

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

#647 - Prepare 2.7.0 release

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

#646 - Update dependencies

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

#645 - Update workflow overview figure & docs

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

#644 - Update pipeline summary report

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

#643 - Fix --dada_ref_tax_custom without --dada_ref_tax_custom_sp

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

#642 - Merging template updates 2.10

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

#641 - Continue analysis even when individual files fail the filtering threshold

Pull Request - State: closed - Opened by sminot about 1 year ago - 5 comments

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

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

#639 - Add GTDB 214.1 for DADA2

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

#638 - Catch error case where 0 reads pass filtering and params.ignore_failed_trimming = True

Pull Request - State: closed - Opened by sminot about 1 year ago - 8 comments

#637 - Add taxonomic classification with kraken2

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

#636 - Adding gtdb release 214 & adding already downloaded database

Issue - State: closed - Opened by x-rv about 1 year ago - 2 comments
Labels: enhancement

#635 - Broken link in README.md

Issue - State: closed - Opened by a4000 about 1 year ago - 2 comments
Labels: bug

#634 - A feature to remove taxa found in controls

Issue - State: open - Opened by skose82 about 1 year ago - 5 comments
Labels: enhancement

#633 - disable GPU for UNIFRAC

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

#632 - Add alpha diversity to sample count correlation to report

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

#631 - Add vsearch uchime_denovo for chimera removal (or flagging)

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

#630 - fix --max_len_asv

Pull Request - State: open - Opened by d4straub about 1 year ago - 3 comments

#629 - Fasta input isnt compatible with most filters

Issue - State: open - Opened by d4straub about 1 year ago - 2 comments
Labels: bug

#628 - Prevent rare error with sample sheet edge case

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

#627 - Cutadapt failing due to renaming of files

Issue - State: closed - Opened by susheelbhanu about 1 year ago - 8 comments
Labels: bug

#626 - RENAME_RAW_DATA_FILES - Process requirement exceeds available CPUs

Issue - State: closed - Opened by amalacrino about 1 year ago - 2 comments

#625 - Manuscript methods section and VSEARCH cluster to pipeline report

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

#624 - fix typo in quick start command

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

#623 - Error in command

Issue - State: closed - Opened by dixi06 over 1 year ago - 2 comments

#622 - add VSEARCH cluster

Pull Request - State: closed - Opened by a4000 over 1 year ago - 1 comment

#621 - Update nextflow_schema.json

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

#620 - Update multiqc methods

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

#619 - add SBDI export and phyloseq output to summary report

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

#618 - Add sintax support for all available databases

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

#617 - Check for SBDI compatibility for sintax

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

#616 - Use nf-validation on samplesheet

Pull Request - State: closed - Opened by d4straub over 1 year ago - 3 comments

#615 - Dev

Pull Request - State: closed - Opened by a4000 over 1 year ago - 2 comments

#614 - Merging template updates 2.9

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

#613 - Potential problem with demultiplexing and proposed solution

Issue - State: open - Opened by a4000 over 1 year ago - 1 comment
Labels: enhancement

#612 - Proposal: Phyloseq R object creation at end of pipeline

Issue - State: closed - Opened by a4000 over 1 year ago - 7 comments
Labels: enhancement

#611 - Proposal: Seqkit stats when demultiplexing

Issue - State: open - Opened by a4000 over 1 year ago - 2 comments
Labels: enhancement

#610 - Proposal: Lowest Common Ancestor (LCA) module for assigning taxonomy

Issue - State: open - Opened by a4000 over 1 year ago - 2 comments
Labels: enhancement

#609 - Proposal: LULU ASV post-clustering curation

Issue - State: closed - Opened by a4000 over 1 year ago - 9 comments
Labels: enhancement

#608 - Proposal: Blastn as an alternative classifier

Issue - State: open - Opened by a4000 over 1 year ago - 6 comments
Labels: enhancement

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

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

#606 - Error at process NFCORE_AMPLISEQ:AMPLISEQ:DADA2_QUALITY (FW)

Issue - State: closed - Opened by BCArg over 1 year ago - 4 comments
Labels: bug

#605 - Sbdi pr2 v5

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

#604 - Release 2.6.1

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

#603 - PREPARE: Release 2.6.1

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

#602 - bump-version-2.7.0dev

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

#601 - Release 2.6.0

Pull Request - State: closed - Opened by d4straub over 1 year ago - 3 comments

#600 - bump-version

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

#599 - PR2 exact species assignment now without taxa ending with sp.

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

#598 - update workflow figure

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

#597 - Change from file size to read counts as sample read threshold

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

#596 - Add PR2 v5.0.0

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

#595 - Restructure reporting of mindepth in QIIME2_DIVERSITY_CORE

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

#594 - fix metadata documentation

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

#593 - Strategy for PR2 species assignments

Issue - State: closed - Opened by andand over 1 year ago - 7 comments
Labels: enhancement

#592 - Documentation error: "Metadata files are not required to have additional metadata columns"

Issue - State: closed - Opened by d4straub over 1 year ago - 1 comment
Labels: bug

#591 - Update unite to version 9.0

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

#589 - QIIME2_DIVERSITY_CORE gaps in mindepth piecewise

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

#588 - Use new PR2 release for 18S (PR2 version 5.0.0)

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

#587 - The pipeline has been running and staying on the interface

Issue - State: closed - Opened by freemutation over 1 year ago - 4 comments
Labels: bug

#586 - activate codon filter and use pandas instead of QIIME2 environment

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

#585 - docker cutadapt file not found

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

#584 - ERROR about NFCORE_AMPLISEQ:AMPLISEQ:PICRUST

Issue - State: closed - Opened by linshizuowei over 1 year ago - 4 comments
Labels: bug

#583 - Bad file descriptor

Issue - State: closed - Opened by weber8thomas over 1 year ago - 4 comments
Labels: bug

#582 - fix diversity analysis

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

#581 - Error executing Ampliseq through pbs/Torque executor

Issue - State: closed - Opened by pehenrique over 1 year ago - 5 comments
Labels: bug

#580 - Feat/init ci nf test

Pull Request - State: closed - Opened by sateeshperi over 1 year ago - 8 comments
Labels: enhancement

#579 - Error locating home in single-end analysis

Issue - State: closed - Opened by pehenrique over 1 year ago - 5 comments
Labels: bug

#578 - Nf core template merge 2.8

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

#577 - Add sintax

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

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

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

#575 - Filter codon

Pull Request - State: closed - Opened by lokeshbio over 1 year ago - 10 comments

#574 - Add UNITE 9.0 databases

Issue - State: closed - Opened by prototaxites over 1 year ago - 5 comments
Labels: enhancement

#573 - fix single end empty file handling

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

#572 - Parser error for single-end data

Issue - State: closed - Opened by lch14forever over 1 year ago - 2 comments
Labels: bug

#571 - Option to filter low-abundant ASVs before running QIIME2_ANCOM_ASV

Issue - State: closed - Opened by SergeWielhouwer over 1 year ago - 6 comments
Labels: enhancement

#570 - nf-test-init-config-pipeline-minimal-tests-snaps

Pull Request - State: closed - Opened by sateeshperi over 1 year ago - 5 comments
Labels: WIP

#569 - Make header in overall_summary consistent

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

#568 - Filter COI ASV sequences based on their length and codons

Pull Request - State: closed - Opened by lokeshbio over 1 year ago - 8 comments

#567 - use phylogenetic placement output in qiime

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

#566 - added description to --exclude_taxa param

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

#565 - Add more details on exclude taxa 559

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

#564 - Add phylogenetic placement

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

#563 - add ref tax abbreviation to DADA2 output tables

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

#562 - Phylogenetic placement part 2

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

#561 - Phylo placement part 1

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

#560 - Add classifier name and database name to output file names

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

#559 - Add more details on --exclude_taxa value taxonomy format

Issue - State: closed - Opened by Ste40 over 1 year ago - 2 comments
Labels: documentation

#558 - Pipeline summary report

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 8 comments

#557 - Feature/summary report

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

#556 - Filtering low read count samples during QC

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

#555 - how did the pipeline filter the "filtered-table.qza"

Issue - State: closed - Opened by bark9299 over 1 year ago - 2 comments