Merge branch 'dev' into improve-database-handling

CHANGELOG.md

@@ -11,9 +11,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#422](https://github.com/nf-core/mag/pull/422) - Adds support for normalization of read depth with BBNorm (added by @erikrikarddaniel and @fabianegli)
 - [#439](https://github.com/nf-core/mag/pull/439) - Adds ability to enter the pipeline at the binning stage by providing a CSV of pre-computed assemblies (by @prototaxites)
 - [#459](https://github.com/nf-core/mag/pull/459) - Adds ability to skip damage correction step in the ancient DNA workflow and just run pyDamage (by @jfy133)
-- [#364](https://github.com/nf-core/mag/pull/364) - Added geNomad nf-core modules for identifying viruses in assemblies (by @PhilPalmer and @CarsonJM)
-- [#437](https://github.com/nf-core/mag/pull/429) - `--gtdb` parameter is split into `--skip_gtdbtk` and `--gtdb_db` to allow finer control over GTDB database retrieval (by @jfy133)
-- [#437](https://github.com/nf-core/mag/pull/429) - `--gtdb_db` also now supports directory input of an pre-uncompressed GTDB archive directory (by @jfy133)
+- [#364](https://github.com/nf-core/mag/pull/364) - Adds geNomad nf-core modules for identifying viruses in assemblies (by @PhilPalmer and @CarsonJM)
+- [#481](https://github.com/nf-core/mag/pull/481) - Adds MetaEuk for annotation of eukaryotic MAGs, and MMSeqs2 to enable downloading databases for MetaEuk (by @prototaxites)
+- [#437](https://github.com/nf-core/mag/pull/429) - `--gtdb_db` also now supports directory input of an pre-uncompressed GTDB archive directory (reported by @alneberg, fix by @jfy133)
 
 ### `Changed`
 
@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#442](https://github.com/nf-core/mag/pull/442) - Remove warning when BUSCO finds no genes in bins, as this can be expected in some datasets (reported by @Lumimar, fix by @jfy133).
 - [#444](https://github.com/nf-core/mag/pull/444) - Moved BUSCO bash code to script (by @jfy133)
 - [#428](https://github.com/nf-core/mag/pull/429) - Update to nf-core 2.9 `TEMPLATE` (by @jfy133)
+- [#437](https://github.com/nf-core/mag/pull/429) - `--gtdb` parameter is split into `--skip_gtdbtk` and `--gtdb_db` to allow finer control over GTDB database retrieval (fix by @jfy133)
 
 ### `Fixed`
 

CITATIONS.md

@@ -94,6 +94,14 @@
 
   > Kang, D. D., Li, F., Kirton, E., Thomas, A., Egan, R., An, H., & Wang, Z. (2019). MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ, 7, e7359. doi: 10.7717/peerj.7359.
 
+- [MetaEuk](https://doi.org/10.1186/s40168-020-00808-x)
+
+> Levy Karin, E., Mirdita, M. & Söding, J. MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome 8, 48 (2020). https://doi.org/10.1186/s40168-020-00808-x
+
+- [MMseqs2](https://www.nature.com/articles/nbt.3988)
+
+> Steinegger, M., Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol 35, 1026–1028 (2017). https://doi.org/10.1038/nbt.3988
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

conf/modules.config

@@ -471,7 +471,7 @@ process {
     withName: PROKKA {
         ext.args   = "--metagenome"
         publishDir = [
-            path: { "${params.outdir}/Prokka/${meta.assembler}" },
+            path: { "${params.outdir}/Annotation/Prokka/${meta.assembler}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -489,7 +489,7 @@ process {
     withName: PRODIGAL {
         ext.args   = "-p meta"
         publishDir = [
-            path: { "${params.outdir}/Prodigal/${meta.assembler}/${meta.id}" },
+            path: { "${params.outdir}/Annotation/Prodigal/${meta.assembler}/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -726,6 +726,26 @@ process {
         ext.prefix = "tiara_summary"
     }
 
+    withName: MMSEQS_DATABASES {
+        ext.prefix = { "${params.metaeuk_mmseqs_db.replaceAll("/", "-")} "}
+        publishDir = [
+            path: { "${params.outdir}/Annotation/mmseqs_db/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_mmseqs_db
+        ]
+    }
+
+    withName: METAEUK_EASYPREDICT {
+        ext.args   = ""
+        ext.prefix = { "${meta.id}" }
+        publishDir = [
+            path: { "${params.outdir}/Annotation/MetaEuk/${meta.assembler}/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },

conf/test_adapterremoval.config

@@ -23,6 +23,7 @@ params {
     input                       = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.euk.csv'
     centrifuge_db               = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_cf.tar.gz"
     kraken2_db                  = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_kraken.tgz"
+    metaeuk_db                  = "https://github.com/nf-core/test-datasets/raw/modules/data/proteomics/database/yeast_UPS.fasta"
     skip_krona                  = true
     min_length_unbinned_contigs = 1
     max_unbinned_contigs        = 2