Merge pull request #394 from jfy133/add-gunc

Add GUNC for additional QC

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#366](https://github.com/nf-core/mag/pull/366) - Added CAT_SUMMARISE process and cat_official_taxonomy parameter (by @prototaxites)
 - [#372](https://github.com/nf-core/mag/pull/372) - Allow CAT_DB to take an extracted database as well as a tar.gz file.
 - [#380](https://github.com/nf-core/mag/pull/380) - Added support for saving processed reads (clipped, host removed etc.) to results directory (by @jfy133)
+- [#394](https://github.com/nf-core/mag/pull/394) - Added GUNC for additional chimeric bin/contamination QC (added by @jfy13)
 
 ### `Changed`
 

CITATIONS.md

@@ -62,6 +62,10 @@
 
   > Chaumeil, P. A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2020). GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics , 36(6), 1925–1927. doi: 10.1093/bioinformatics/btz848.
 
+- [GUNC](https://doi.org/10.1186/s13059-021-02393-0.)
+
+  > Orakov, A., Fullam, A., Coelho, A. P., Khedkar, S., Szklarczyk, D., Mende, D. R., Schmidt, T. S. B., and Bork, P.. 2021. “GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes.” Genome Biology 22 (1): 178. doi: 10.1186/s13059-021-02393-0.
+
 - [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)
 
   > Wood, D et al., 2019. Improved metagenomic analysis with Kraken 2. Genome Biology volume 20, Article number: 257. doi: 10.1186/s13059-019-1891-0.

README.md

@@ -34,7 +34,7 @@ The pipeline then:
 - performs assembly using [MEGAHIT](https://github.com/voutcn/megahit) and [SPAdes](http://cab.spbu.ru/software/spades/), and checks their quality using [Quast](http://quast.sourceforge.net/quast)
 - (optionally) performs ancient DNA assembly validation using [PyDamage](https://github.com/maxibor/pydamage) and contig consensus sequence recalling with [Freebayes](https://github.com/freebayes/freebayes) and [BCFtools](http://samtools.github.io/bcftools/bcftools.html)
 - predicts protein-coding genes for the assemblies using [Prodigal](https://github.com/hyattpd/Prodigal)
-- performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), and/or with [CONCOCT](https://github.com/BinPro/CONCOCT), and checks the quality of the genome bins using [Busco](https://busco.ezlab.org/) or [CheckM](https://ecogenomics.github.io/CheckM/).
+- performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), and/or with [CONCOCT](https://github.com/BinPro/CONCOCT), and checks the quality of the genome bins using [Busco](https://busco.ezlab.org/), or [CheckM](https://ecogenomics.github.io/CheckM/), and optionally [GUNC](https://grp-bork.embl-community.io/gunc/).
 - optionally refines bins with [DAS Tool](https://github.com/cmks/DAS_Tool)
 - assigns taxonomy to bins using [GTDB-Tk](https://github.com/Ecogenomics/GTDBTk) and/or [CAT](https://github.com/dutilh/CAT)
 

conf/modules.config

@@ -366,6 +366,33 @@ process {
         ]
     }
 
+    withName: 'GUNC_DOWNLOADDB' {
+        publishDir = [
+            path: { "${params.outdir}/GenomeBinning/QC/GUNC" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.gunc_save_db
+        ]
+    }
+
+    // Make sure to keep directory in sync with gunc_qc.nf
+    withName: 'GUNC_RUN' {
+        publishDir = [
+            path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    // Make sure to keep directory in sync with gunc_qc.nf
+    withName: 'GUNC_MERGECHECKM' {
+        publishDir = [
+            path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: CAT_DB_GENERATE {
         publishDir = [
             path: { "${params.outdir}/Taxonomy/CAT" },