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pipeline halts when quast finds no min length contigs

2

Hi, I'm running mag and have run into a problem where it throws an error and stops running when quast reaches a contig file that has no contigs meeting the...

ivelsko

Help running in offline cluster

3

I need to run *mag* in offline mode and I tried with: ```bash nextflow run $NF/nextflow/nf-core-mag-1.0.0/workflow/main.nf \ --reads '$INPUT/reads/*_R{1,2}.fq.gz' \ --busco_reference $DB/bacteria_odb9.tar.gz \ --outdir out \ --cat_db $DB/CAT_prepare_20190108.tar.gz \ --kraken2_db...

telatin

Update modules that can be replaced by new nf-core modules and port local modules where possible to nf-core.

skrakau

Currently CAT is only applied to MetaBAT bins for taxonomic classification. Maybe it would be useful to apply it on whole assemblies / also on unbinned contigs.

skrakau

This issue summarises the discussion that emerged at the London hackathon concerning a possible merge with [YAMP](https://github.com/alesssia/YAMP) While MAG focuses heavily on assembly, YAMP is assembly-free and focuses on taxonomy...

HadrienG

Set minimal contig length for metaBAT2 to 1,500 if the provided value is smaller

1

### Description of the bug The parameter `--min_contig_size` allows the user to specify the minimal contig length for binning and subsequent analysis. The program metaBAT2 requires a minimal contig length...

alexhbnr

Add Bakta as alternative to Prokka

9

### Description of feature Also recommended by Prokka developer! nf-core module already exists

jfy133

GTDB-TK fails due to insufficient memory

3

### Description of the bug Hi, I have been trying to run the MAG pipeline with the latest version. However, the pipeline is failing at the GTDBTK_Classify step due to...

nayeimkhan

Sharing an issue when I use nf-core/mag pipeline

7

### Description of the bug ``` Caused by Process `NFCORE_MAG:BINNING:MAG_DEPTHS_PLOT (MEGAHIT-MetaBAT2-G3062_unclassified)` terminated with an error exit status (1) Command executed: plot_mag_depths.py --bin_depths MEGAHIT-MetaBAT2-G3062_unclassified-binDepths.tsv --groups sample_groups.tsv --out "MEGAHIT-MetaBAT2-G3062_unclassified-binDepths.heatmap.png" Error executing process...

bbagy

BUSCO creates a huge number of files - add a flag to remove some of these?

4

### Description of feature Somewhere between a bug and a feature request - I'm running the pipeline and have generated 608 bins. I'm now at the BUSCO step and the...

prototaxites