nf-core / mag

Assembly and binning of metagenomes

https://nf-co.re/mag

nf-core/mag Issues

List of tool versions
Closed 22 days ago1
Remove redundant QC checks from WorkFlowMag
Closed 24 days ago1
CAT_DB process has harcoded CAT subdirectory names
Updated a month ago1
Pipeline completed sucessfully, but with errored process(es)
Closed a month ago1
Genome taxnomic classification with Sourmash
Updated a month ago3
Replace CheckM with CheckM2
Updated 2 months ago
Bins in CheckM summary do not match bins in bin depths summary
Updated 2 months ago7
Improve documentation on the effects of completeness/contamination filters
Updated 2 months ago
NFCORE_MAG:MAG:GTDBTK:GTDBTK_CLASSIFYWF fails when all genomes classified by ANI screening step
Updated 2 months ago3
Error in executing PROKKA
Updated 2 months ago4
add diamond support to mag
Updated 2 months ago
CHECKM_LINEAGEWF failing with exit status 1
Closed 2 months ago7
Centrifuge error - (ERR): mkfifo(/tmp/46.inpipe1) failed.
Updated 2 months ago3
Problem with DUMPSOFTWAREVERSIONS
Closed 2 months ago2
ERROR ~ Unknown method invocation `getBaseName` on String type
Closed 3 months ago6
Single end data input
Closed 3 months ago
CONCOCT (slow)
Closed 3 months ago1
Pipeline fails if only CONCOCT is turned on and other binners off
Updated 3 months ago
Add explicit test for single end data
Closed 3 months ago1
Add license headers to all scripts
Closed 3 months ago
Expanded documentation for nf-core/mag use cases & downstream analysis
Updated 3 months ago
Add documentation detailing phageome/virome analysis
Updated 3 months ago
Add coverm/contig and coverm/genome as options for calculating read alignment metrics
Updated 3 months ago
Supplying a directory to --gtdbk-db breaks GTDB-Tk
Closed 3 months ago1
Remove `.ifEmpty([])` from BUSCO_SUMMARY channels
Closed 3 months ago1
CAT_FASTQ does not work with single end data
Closed 3 months ago
Process `NFCORE_MAG:MAG:MEGAHIT` terminated with an error exit status (255)
Closed 3 months ago1
Add StrainXpress assembler
Updated 3 months ago
Please make --binning_map_mode group and --ancient-dna compatible features
Updated 3 months ago1
Unusual Local Storage Path for Pipeline Info Files in nf-core/mag with AWS S3 Outdir
Closed 3 months ago6
CAT is not included in the the `BIN_SUMMARY`
Closed 3 months ago1
Reorder MultiQC sections so all assembly related statistics go together, and all binning statistics go together
Closed 3 months ago1
Output directory MEGAHIT already exists, please change the parameter -o to another value to avoid overwriting.
Closed 4 months ago6
GTDBTK_SUMMARY: Not a valid path ...
Closed 4 months ago5
process GTDBTK_CLASSIFYWF: glob in find command
Closed 4 months ago4
BUSCO db placement files not found
Closed 4 months ago2
Is there any database we need to download?
Updated 4 months ago12
Can't complete test_full, Error executing process > 'NFCORE_MAG:MAG:PROKKA
Closed 4 months ago6
Error with classification
Closed 4 months ago2
BUSCO summary fails
Closed 4 months ago5
CONCOCT - OpenBLAS Warning
Updated 5 months ago3
Tiara is not included in bin_summary
Updated 6 months ago1
MetaBAT2 bins folder not created, and MAGs from metabat2 not saved.
Closed 6 months ago1
Pipeline Execution Failure: MissingMethodException for LinkedList.getFileSystem in Nextflow 23.10.0
Closed 6 months ago5
Consider using `collectFile` to optimise aggregating of results of bin statistics steps
Updated 6 months ago
SPAdes out of memory
Closed 7 months ago6
--postbinning_input to include only bins (no unassembled contigs)
Updated 7 months ago
GTDB-TK can't find tree and msa output files
Closed 7 months ago1
Tiara log dir is empty, and tiara summary file not in Tiara directory
Closed 7 months ago
Depth PNG file names have `null` in them
Closed 7 months ago