A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hello,

I have observed that the binning step + DAS produced 436 refined MAGs but the taxonomy step only contains 380 MAGs. Why the difference? was there filtering?

```nextflow run nf-core/mag -r 4.0.0  \
	--input samplesheet.csv \
	--outdir results \
	--gtdb_db /reference/KSL/gtdb-tk/release220/ \
	--skip_spades true --skip_concoct true \
	--prokka_compliance_centre NCBI --prokka_with_compliance true \
	--refine_bins_dastool true \
	--binqc_tool checkm2 \
	--coassemble_group true –binning_map_mode all \
	--postbinning_input both```

Most likley due to: <https://nf-co.re/mag/5.4.0/parameters/#gtdbtk_min_completeness> and  <https://nf-co.re/mag/5.4.0/parameters/#gtdbtk_max_contamination>

We filter out low quality mags as GTDBTk is extremely compute hungry, so we make it less expensive by removing MAgs that likely are not worth analysing downstream (based on completeness/contamination metrics anyway)