Add screening params in multiqc

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added `--day0_label` and `FluteMLE` for MLE data [#126](https://github.com/nf-core/crisprseq/pull/126)
 - Template update to 2.13.1 ([#124](https://github.com/nf-core/crisprseq/pull/124))
 - Metromap added in the docs ([#128](https://github.com/nf-core/crisprseq/pull/128))
+- Added MAGeCK count table in the multiqc ([#131](https://github.com/nf-core/crisprseq/pull/131))
 
 ### Fixed
 

README.md

@@ -63,12 +63,14 @@ For crispr screening:
 
 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 2. Read mapping ([`MAGeCK count`](https://sourceforge.net/p/mageck/wiki/usage/#count))
+   - ([`MAGeCK count`](https://github.com/lh3/minimap2), _default_)
+   - ([`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
 3. Optional: CNV correction and normalization with ([`CRISPRcleanR`](https://github.com/francescojm/CRISPRcleanR))
 4. Rank sgRNAs and genes ;
    a. ([MAGeCK test](https://sourceforge.net/p/mageck/wiki/usage/#test))
    b. ([MAGeCK mle](https://sourceforge.net/p/mageck/wiki/Home/#mle))
    c. ([BAGEL2](https://github.com/hart-lab/bagel))
-5. Visualise analysis
+5. Visualize analysis
 
 ## Usage
 

assets/multiqc_config.yml

@@ -144,6 +144,52 @@ custom_data:
         min: 0
         scale: "RdYlGn"
 
+  # MAGeCK count table
+  mageck_count:
+    id: "mageck_count"
+    section_name: "MAGeCK count table"
+    plot_type: "table"
+    description: |
+      Table showing count quality for MAGeCK count.
+    pconfig:
+      id: "mageck_count"
+      namespace: "MAGeCK count table"
+      table_title: "MAGeCK count table"
+    headers:
+      File:
+        title: "File"
+        description: "File name"
+      Label:
+        title: "Label"
+        description: "Label name"
+        format: "{:,.0f}"
+      Reads:
+        title: "Reads"
+        description: "Number of reads"
+        format: "{:,.0f}"
+      Mapped:
+        title: "Mapped"
+        description: "Number of reads mapped"
+        format: "{:,.0f}"
+      Percentage:
+        title: "Percentage mapped from 0 to 1 (100%)"
+        description: "Percentage mapped"
+        max: 1
+        min: 0
+      TotalsgRNAs:
+        title: "Total number of sgRNAs in the library"
+        description: "Total number of sgRNAs in the library"
+        format: "{:,.0f}"
+      Zerocounts:
+        title: "Total number of missing sgRNAs"
+        description: "sgRNAs that have 0 counts, recommended: no more than 1%)"
+        format: "{:,.0f}"
+      GiniIndex:
+        title: "Gini Index"
+        description: "Measure of statistical dispersion. A smaller value indicates more eveness of the count distribution."
+        max: 1
+        min: 0
+
 sp:
   edition_plot:
     fn: "*_edits.csv"
@@ -153,11 +199,14 @@ sp:
     fn: "*_reads-summary.csv"
   cutadapt:
     fn: "*.cutadapt.log"
+  mageck_count:
+    fn: "*.countsummary.txt"
 
 # Define the order of sections
 module_order:
   - fastqc
   - cutadapt
+  - mageck_count
   - custom_content
 
 # Set the order of custom code plots and tables

workflows/crisprseq_screening.nf

@@ -161,6 +161,7 @@ workflow CRISPRSEQ_SCREENING {
         )
 
         ch_versions = ch_versions.mix(MAGECK_COUNT.out.versions.first())
+        ch_multiqc_files = ch_multiqc_files.mix(MAGECK_COUNT.out.summary.collect{it[1]})
 
         MAGECK_COUNT.out.count.map {
         it -> it[1]