Add BAGEL2 functionality

CHANGELOG.md

@@ -9,9 +9,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Template update v2.9 ([#52](https://github.com/nf-core/crisprseq/pull/52))
 - Use `Channel.fromSamplesheet()` from `nf-validation` to validate input sample sheets and create an input channel ([#58](https://github.com/nf-core/crisprseq/pull/58))
+- BAGEL2 as a module which detects gene essentiality ([#60](https://github.com/nf-core/crisprseq/pull/60))
 
 ### Fixed
 
+- Change to `process_high` for the mageck mle module ([#60](https://github.com/nf-core/crisprseq/pull/60)
 - Summary processes don't modify the input file anymore, allowing resuming these processes ([#66](https://github.com/nf-core/crisprseq/pull/66))
 - Do not stash unexistent files, use empty lists instead. Fixes AWS tests ([#67](https://github.com/nf-core/crisprseq/pull/67))
 - Rename process `merging_summary` to `preprocessing_summary` to improve clarity ([#69](https://github.com/nf-core/crisprseq/pull/69))

CITATIONS.md

@@ -63,6 +63,10 @@
 
   > Li, W. et al. Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR. Genome Biology 16, 281, doi:10.1186/s13059-015-0843-6 (2015).
 
+- [BAGEL2](https://pubmed.ncbi.nlm.nih.gov/33407829/)
+
+  > Kim E, Hart T. Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier. Genome Med. 2021 Jan 6;13(1):2. doi: 10.1186/s13073-020-00809-3. PMID: 33407829; PMCID: PMC7789424.
+
 - [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
 
   > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

assets/schema_input.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+   "$schema": "http://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/crisprseq/master/assets/schema_input.json",
     "title": "nf-core/crisprseq pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
@@ -30,8 +30,6 @@
             "condition": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "enum": ["control", "treatment"],
-                "errorMessage": "Condition name must be one of 'control' or 'treatment'",
                 "meta": ["condition"]
             },
             "reference": {