Merge pull request #8 from nf-core/dev

Dev

docs/output.md

@@ -166,13 +166,27 @@ Sequencing depth per contig and sample is generated by `jgi_summarize_bam_contig
 
 - `<assembler>-<assembly>-depth.txt.gz`: Sequencing depth for each contig and sample, only for short reads.
 
-### Metabat
+### MetaBAT2
 
-[metabat](https://bitbucket.org/berkeleylab/metabat) recovers genome bins (that is, contigs/scaffolds that all belongs to a same organism) from metagenome assemblies. Additionally, Quast is run again on all the genome bins.
+[MetaBAT2](https://bitbucket.org/berkeleylab/metabat) recovers genome bins (that is, contigs/scaffolds that all belongs to a same organism) from metagenome assemblies.
 
-**output directory: `results/GenomeBinning/MetaBat2`**
+**output directory: `results/GenomeBinning/MetaBAT2`**
 
-- `*.fa`: Genome bins retrieved from the different input assemblies
+- `$assembler-$sample.*.fa`: Genome bins retrieved from input assembly
+- `$assembler-$sample.unbinned.*.fa`: Contigs that were not binned with other contigs but considered interesting. By default, these are at least 1 Mbp (`--min_length_unbinned_contigs`) in length and at most the 100 longest contigs (`--max_unbinned_contigs`) are reported.
+
+All the files in this folder will be assessed by Quast and Busco.
+
+**output directory: `results/GenomeBinning/MetaBAT2/discarded`**
+
+- `*.lowDepth.fa`: Low depth contigs that are filtered by MetaBat2
+- `*.tooShort.fa`: Too short contigs that are filtered by MetaBat2
+- `*.unbinned.pooled.fa`: Pooled unbinned contigs equal or above `--min_contig_size`, by default 1500 bp.
+- `*.unbinned.remaining.fa`: Remaining unbinned contigs below `--min_contig_size`, by default 1500 bp, but not in any other file.
+
+All the files in this folder contain small and/or unbinned contigs that are not further processed.
+
+Files in these two folders contain all contigs of an assembly.
 
 ### Busco