Ecosyste.ms: Issues

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GitHub / nf-core/mag issues and pull requests

#535 - CAT is not included in the the `BIN_SUMMARY`

Issue - State: open - Opened by maxibor about 1 year ago
Labels: bug, enhancement

#534 - Patch for 2.5.0 release

Pull Request - State: open - Opened by maxibor about 1 year ago - 2 comments

#533 - Fix metaBAT2 bin publishing

Pull Request - State: closed - Opened by jfy133 about 1 year ago - 2 comments

#532 - Consider using `collectFile` to optimise aggregating of results of bin statistics steps

Issue - State: open - Opened by jfy133 about 1 year ago
Labels: enhancement

#531 - MetaBAT2 bins folder not created, and MAGs from metabat2 not saved.

Issue - State: open - Opened by patriciatran about 1 year ago - 1 comment
Labels: bug

#530 - ERROR ~ Unknown method invocation `getBaseName` on String type

Issue - State: open - Opened by PPpissar over 1 year ago - 2 comments
Labels: bug

#529 - Remove `.ifEmpty([])` from BUSCO_SUMMARY channels

Issue - State: open - Opened by jfy133 over 1 year ago
Labels: bug

#528 - --postbinning_input to include only bins (no unassembled contigs)

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

#527 - SPAdes out of memory

Issue - State: closed - Opened by s-junguy over 1 year ago - 6 comments
Labels: bug

#526 - Bump versions post release

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#525 - GTDB-TK can't find tree and msa output files

Issue - State: closed - Opened by jfy133 over 1 year ago - 1 comment
Labels: bug

#524 - Release: 2.5.0

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 2 comments

#523 - Temp full test

Pull Request - State: open - Opened by jfy133 over 1 year ago - 1 comment
Labels: do not merge

#522 - Fix null in depth PNG files

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 3 comments

#521 - Use correct meta for depth plot input

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 3 comments
Labels: do not merge

#520 - Fix Tiara publishing files

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 8 comments

#519 - Tiara log dir is empty, and tiara summary file not in Tiara directory

Issue - State: closed - Opened by jfy133 over 1 year ago
Labels: bug

#518 - Depth PNG file names have `null` in them

Issue - State: closed - Opened by jfy133 over 1 year ago
Labels: bug

#517 - CONCOCT related bins not present in DASTool output (test profile)

Issue - State: closed - Opened by jfy133 over 1 year ago - 1 comment
Labels: bug

#516 - Fix MEGAHIT process on resume

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

#515 - Fix missing GUNC overwriting #514

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 2 comments

#514 - Fix missing concoct globs

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 4 comments

#513 - Post 2.4.0 release version bump

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#512 - Update CHANGELOG after registry update (missed in previous PR)

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

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

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 2 comments

#510 - CONCOCT missing in globs in downstream processes of modules.conf

Issue - State: closed - Opened by jfy133 over 1 year ago - 1 comment
Labels: bug

#509 - Registry update for all modules

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 4 comments

#508 - 2.4 review comments

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#507 - Investigate use of specifying `size` in groupTuple operations to improve efficiency

Issue - State: open - Opened by jfy133 over 1 year ago
Labels: enhancement

#506 - Error with SPAdes (Exit status 250)

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

#505 - Remove inefficient basic file handling pipeline steps

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

#504 - Allow local databases to be used for kraken2, centrifuge, and busco

Pull Request - State: closed - Opened by gregorysprenger over 1 year ago - 15 comments
Labels: do not merge, ready to review

#502 - GUNC output overwriting itself

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

#499 - Release 2.4

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 3 comments

#498 - Allow decompressed databases to be used for gtdb, kraken2, centrifuge, and busco

Issue - State: closed - Opened by gregorysprenger over 1 year ago - 2 comments
Labels: enhancement, WIP

#496 - Fixed Update description of additional Bowtie2 and SPAdes parameters …

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

#495 - Fix mmseqs_databases prefix

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

#494 - Add ability to save assembly-mapped reads

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 3 comments

#493 - fix: metabat2 failed on fusion file systems

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

#492 - Allow database input for busco to be directory

Issue - State: closed - Opened by jfy133 over 1 year ago - 4 comments
Labels: enhancement

#491 - Update concoct

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

#490 - Issues running testprofile. "BUSCO analysis failed for some unknown reason!"

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

#489 - Fix for `NFCORE_MAG:MAG:CAT_SUMMARY input file name collision`

Pull Request - State: closed - Opened by maxibor over 1 year ago - 24 comments
Labels: ready to review

#488 - Add option to specify the minimal contig length used for the pyDamage analysis

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

#487 - Add option to export BAM file with reads aligned against the contigs to results folder

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

#486 - Fix Tiara + Concoct bug

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

#485 - Add missing tag and label to tiara_classify

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

#484 - BUSCO batch mode

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

#483 - consider adding CheckM2 to the pipeline

Issue - State: open - Opened by jfy133 over 1 year ago

#482 - How to run in an offline environment?

Issue - State: closed - Opened by IvanWoo22 over 1 year ago - 3 comments
Labels: bug

#481 - Add MetaEuk for Eukaryotic genome annotation

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

#480 - Fix meta map stability

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#479 - Resume results in inconsistent errors at MAG_DEPTHS

Issue - State: closed - Opened by jfy133 over 1 year ago - 1 comment
Labels: bug

#478 - ERROR nextflow.cli.Launcher - Is a directory

Issue - State: closed - Opened by Pandapip1 over 1 year ago - 9 comments
Labels: bug

#477 - Standardises GTDB execution and allow pre-uncompressed GTDB input

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 17 comments

#476 - Missing or corrupted meta map in short reads channel?

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

#475 - Specify GUNC mergecheckm file on module load rather than directory

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#474 - `CAT_SUMMARY` fails due to input filename collision

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

#473 - Move binning entry test to binrefinement test, and fix binning entry+ concoct bug

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

#472 - PyDamage analyze error

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

#471 - Update containers paths for all modules to use registry variable

Issue - State: open - Opened by jfy133 over 1 year ago
Labels: enhancement

#470 - Skip binning prep when no binning/aDNA

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 5 comments

#469 - Please delete this issue

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

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

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 3 comments

#466 - memory allocation fails

Issue - State: closed - Opened by mtva0001 over 1 year ago - 7 comments
Labels: bug

#465 - BOWTIE2 task failing when scratch set as /tmp

Issue - State: open - Opened by CarstenBaker over 1 year ago - 17 comments
Labels: bug

#464 - Move input parameter validats in lib/WorkflowMAg to nextflow schema

Issue - State: open - Opened by jfy133 over 1 year ago
Labels: enhancement, low-priority

#463 - Pull in recent patch release changes from master into dev

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 10 comments

#462 - CAT_DB_GENERATE issues

Issue - State: open - Opened by prototaxites over 1 year ago - 2 comments
Labels: bug

#461 - Patch 2.3.2

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 3 comments

#460 - [DO NOT MERGE] Pseudo-PR to test for conflicts

Pull Request - State: closed - Opened by jfy133 over 1 year ago

#459 - Make ancient DNA damage correction optional

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 3 comments

#458 - Patch release: Fix #449 (wrong contigs from aDNA workflow going to binning)

Pull Request - State: closed - Opened by maxibor over 1 year ago - 7 comments

#457 - Error executing process > 'NFCORE_MAG:MAG:QUAST_BINS (SPAdes-MaxBin2-test_minigut_sample2)'

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

#455 - Make all pipeline steps opt-in

Issue - State: open - Opened by prototaxites over 1 year ago - 8 comments
Labels: enhancement

#454 - gtdbtk classify_wf did not produce *.classify.tree output

Issue - State: open - Opened by FranciscoDA over 1 year ago - 1 comment
Labels: bug

#453 - Parse customized parameters to module KRAKEN2

Issue - State: open - Opened by lam-c over 1 year ago - 3 comments
Labels: enhancement

#452 - Host removal parameter - pre-built bowtie2 index

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

#451 - Fix AncientDNA results files overwriting

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#449 - Genome binning is performed on uncorrected contigs when selecting the ancient DNA subworkflow

Issue - State: closed - Opened by alexhbnr over 1 year ago - 4 comments
Labels: bug, question

#448 - update gtdbtk module

Pull Request - State: closed - Opened by alxndrdiaz over 1 year ago - 3 comments
Labels: enhancement

#447 - Remove default: None from parameter schema

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

#446 - Move code from main workflow to subworkflows

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

#445 - Fix bug in assembly input code

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

#444 - Move BUSCO bash code a script

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 3 comments

#443 - terminated with exit status 255 at GUNZIP BINS singularity

Issue - State: closed - Opened by aquaiser over 1 year ago - 3 comments
Labels: support

#442 - Remove BUSCO warning about no matches found

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 2 comments

#441 - Deactivate CONCOCT to make reasonable AWS full test run time

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#440 - Add option to split SPAdes read correction into separate process or enable SPAdes checkpoints

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

#439 - Add entry point to pipeline at binning stage

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

#438 - Fix GTDB version in consistency

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#437 - Host removal on assembly contigs

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

#436 - Make GTDB downloading skippable using standard parameter name

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 5 comments

#435 - Adds support for run merging for multi-run samples

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 20 comments

#434 - Fix samplesheet path from s3 to GH

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#433 - tax_classification_taxids is the channel that needs collect for CAT_summary

Pull Request - State: closed - Opened by maxibor over 1 year ago - 8 comments
Labels: bug