metagenome-atlas/atlas issues and pull requests

#737 - log names inconsistencies

Issue - State: open - Opened by strejcem about 1 month ago
Labels: Feature request

#736 - feat: Add Public init using Kingfisher

Pull Request - State: open - Opened by SilasK about 1 month ago - 1 comment

#735 - style: code correctly spelled

Pull Request - State: open - Opened by SilasK 2 months ago - 1 comment

#734 - feat: GTDB v9 R220, Spades v4

Pull Request - State: closed - Opened by SilasK 2 months ago - 1 comment

#733 - Error in rule `dram_download`

Issue - State: closed - Opened by bharat1912 2 months ago - 2 comments

#731 - Error in rule

Issue - State: open - Opened by bharat1912 2 months ago - 5 comments

#730 - feat: GTDB v9 Refseq 220

Pull Request - State: closed - Opened by SilasK 3 months ago

#729 - chore(main): release 2.18.2

Pull Request - State: closed - Opened by github-actions[bot] 3 months ago - 1 comment
Labels: autorelease: tagged

#728 - chore(master): release 2.18.2

Pull Request - State: closed - Opened by github-actions[bot] 3 months ago
Labels: autorelease: pending

#727 - Fix dram

Pull Request - State: closed - Opened by SilasK 3 months ago

#726 - Use kingfisher for public init

Pull Request - State: open - Opened by SilasK 3 months ago - 1 comment

#725 - Gtdb v9

Pull Request - State: open - Opened by SilasK 3 months ago - 1 comment

#723 - Snake8

Pull Request - State: open - Opened by SilasK 4 months ago

#722 - Error in rule build_qc_report: ModuleNotFoundError: No module named 'numpy._version'

Issue - State: closed - Opened by the-eon-flux 4 months ago - 2 comments

#721 - Support for highly accurate long reads?

Issue - State: closed - Opened by MrTomRod 5 months ago - 1 comment
Labels: Feature request

#720 - What does "max" in the combined_contig_stats.tsv mean?

Issue - State: closed - Opened by s-junguy 5 months ago - 1 comment
Labels: Feature request

#719 - plans for supporting fungi

Issue - State: closed - Opened by jotech 5 months ago - 5 comments
Labels: Feature request, stale

#718 - Error during DRAM download; processing vogdb

Issue - State: closed - Opened by abarilo 5 months ago - 6 comments

#717 - Error in rule get_bins: only 1 conting found in samples

Issue - State: closed - Opened by anbadilla 6 months ago

#714 - Update multiqc wrapper to newest version.

Pull Request - State: closed - Opened by njohner 8 months ago - 1 comment

#713 - Correction of typos

Pull Request - State: closed - Opened by Waschina 9 months ago - 3 comments

#712 - Public init v2

Pull Request - State: closed - Opened by mortonjt 9 months ago - 1 comment

#710 - MissingOutputException

Issue - State: closed - Opened by topfm 10 months ago - 2 comments

#708 - Error in rule run_spades

Issue - State: closed - Opened by s-junguy 11 months ago - 19 comments

#707 - Error in rule

Issue - State: closed - Opened by yustinus1 11 months ago - 5 comments
Labels: stale

#706 - Disk_mem not sufficient

Issue - State: closed - Opened by SilasK 11 months ago - 6 comments

#705 - Run atlas genomes without the taxonomy output

Issue - State: closed - Opened by AnneliektH 11 months ago - 1 comment
Labels: Feature request

#704 - atlas init-public no such command

Issue - State: closed - Opened by claireewilliams 11 months ago - 2 comments
Labels: stale

#703 - Creating envs (--conda-create-envs-only) is running without error, but not creating envs

Issue - State: closed - Opened by LLansing 11 months ago - 1 comment

#702 - Error in rule multiqc_mapping_genome due to incontability with python 3.12

Issue - State: open - Opened by valery-shap 11 months ago - 11 comments
Labels: stale

#701 - Setting eggNOG_use_virtual_disk to true

Issue - State: closed - Opened by Roxy-mzh 11 months ago - 4 comments
Labels: Feature request

#700 - atlas downdload fail

Issue - State: closed - Opened by jowodo 12 months ago - 6 comments

#699 - Ci opt

Pull Request - State: closed - Opened by SilasK 12 months ago

#698 - Error in localrule parse_vamb_output:

Issue - State: closed - Opened by the-eon-flux about 1 year ago - 5 comments

#697 - Qc reads from init not in qc reads

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

#696 - atlas metatranscriptome data - MissingOutputException in rule run_spades

Issue - State: closed - Opened by jilldv about 1 year ago - 19 comments

#695 - NaNs in samples.tsv

Issue - State: closed - Opened by AroArz about 1 year ago - 6 comments
Labels: enhancement

#693 - Error in rule run_vamb

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

#692 - Error in rule

Issue - State: closed - Opened by bbagy about 1 year ago - 11 comments
Labels: stale

#691 - I am alway stuck at 3% done

Issue - State: closed - Opened by Patcha-pou about 1 year ago - 2 comments
Labels: stale

#690 - Process for determining % of data binned?

Issue - State: closed - Opened by maggieweng about 1 year ago - 2 comments
Labels: stale

#689 - genome_filter_criteria is printed on two lines

Issue - State: closed - Opened by SilasK about 1 year ago - 1 comment
Labels: stale

#688 - Question about co-binning behavior

Issue - State: closed - Opened by mladen5000 about 1 year ago - 8 comments
Labels: stale

#687 - Output directory

Issue - State: closed - Opened by susheelbhanu about 1 year ago - 2 comments
Labels: Feature request

#686 - Error in rule

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

#685 - Error in rule rename_genomes

Issue - State: closed - Opened by XC-Zhai about 1 year ago - 10 comments

#684 - Seperate sampletable in new smk

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

#683 - Enable running cobinning on different bingroups

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

#682 - ci: use micromamba

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

#681 - Convert mem_mb value from gb to mb for select rules

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

#680 - Reuse existing genome taxonomy database (gtdb) when installing conda environments

Issue - State: closed - Opened by jotech about 1 year ago - 2 comments
Labels: Feature request

#678 - Fixed pandas dependency for instrain

Pull Request - State: closed - Opened by mladen5000 about 1 year ago - 1 comment

#676 - Define default resources

Issue - State: closed - Opened by SilasK over 1 year ago - 15 comments
Labels: Feature request, stale

#675 - download wrapper on head node

Issue - State: closed - Opened by jotech over 1 year ago - 8 comments
Labels: stale

#674 - Added certificate for gtdb_v08

Pull Request - State: closed - Opened by mladen5000 over 1 year ago

#673 - Error in rule download_gtdb

Issue - State: closed - Opened by mladen5000 over 1 year ago - 1 comment

#672 - skani parameter usage in atlas derep

Issue - State: closed - Opened by bluenote-1577 over 1 year ago - 2 comments

#671 - Move config folder outside

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

#669 - ci: store genecatalog envs

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

#668 - Error in rule rule apply_quality_filter

Issue - State: closed - Opened by jotech over 1 year ago - 8 comments

#667 - Improvement of offline cluster mode

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

#666 - Improvement of offline cluster mode

Issue - State: closed - Opened by jotech over 1 year ago - 2 comments
Labels: Feature request

#665 - Error in rule run_das_tool for test

Issue - State: closed - Opened by XC-Zhai over 1 year ago - 5 comments

#664 - Error in rule dram_download

Issue - State: closed - Opened by jotech over 1 year ago - 21 comments

#663 - Genome dereplication using skani

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

#662 - clean up

Issue - State: closed - Opened by slambrechts over 1 year ago - 3 comments

#661 - Fixed error in rule combine_egg_nogg_annotations:

Pull Request - State: closed - Opened by mladen5000 over 1 year ago - 2 comments

#660 - Patch 1

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

#658 - specify config file directly to dram

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

#657 - checmk2 ERROR: DIAMOND database not found

Issue - State: closed - Opened by JustinGibbons over 1 year ago - 7 comments

#656 - Neweggnog

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

#655 - Error in rule get_all_modules

Issue - State: closed - Opened by mladen5000 over 1 year ago - 12 comments
Labels: stale

#654 - Error in rule DRAM_destill

Issue - State: closed - Opened by mladen5000 over 1 year ago - 1 comment

#653 - Error in rule combine_egg_nogg_annotations

Issue - State: closed - Opened by mladen5000 over 1 year ago - 2 comments
Labels: stale

#652 - Add missing concoct environment file

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

#651 - Progressing despite individual binner failure

Issue - State: open - Opened by mladen5000 over 1 year ago - 3 comments
Labels: Feature request, keep

#650 - Don't use map quality filtering in binning

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

#649 - fixed typo

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

#648 - gtdb v8

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

#647 - Use minimum mapping quality in pileup

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

#646 - WorkflowError: Failed to obtain job status.

Issue - State: closed - Opened by irvinng98 over 1 year ago - 5 comments
Labels: stale

#645 - Error in rule get_read_stats and run_decontamination during run qc

Issue - State: closed - Opened by lineroager over 1 year ago - 4 comments

#643 - docs: update gene catalog

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

#642 - fix gene_info.parquet

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

#641 - fix errors_due to pie

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

#640 - median_coverage.h5 ERROR

Issue - State: closed - Opened by luozhy88 over 1 year ago - 4 comments

#639 - UPDATE GIHUB WORKFLOW

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

#638 - use cache package

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

#637 - Update python-package-conda.yml

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

#635 - Error in rule apply_quality_filter

Issue - State: closed - Opened by johnne over 1 year ago - 1 comment

#634 - atlas init cannot find template_config.yaml

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

#633 - make gunc optional

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

#632 - Dram on genecatalog

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

#631 - Error in rule DRAM_destill

Issue - State: closed - Opened by mladen5000 over 1 year ago - 4 comments

#630 - Error in rule concat_annotations

Issue - State: closed - Opened by mladen5000 over 1 year ago - 3 comments
Labels: stale

GitHub / metagenome-atlas/atlas issues and pull requests