nf-cmgg · nvnieuwk · Jun 24, 2025 · May 21, 2025 · May 26, 2025 · May 26, 2025
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -37,9 +37,36 @@ mosdepth_config:
     - "HLA*"
     - "chrM"
     - "chrEBV"
-
-custom_data:
-  msisensorpro_summary:
-    pattern: "*_unstable"  # or your actual filename pattern
-    section_name: "MSIsensorPro Summary"
-    description: "Summary of MSI sites per sample"
+
+table_cond_formatting_rules:
+  msiSensorPro_all_table:
+    pass:
+      - s_contains: "Stable"
+    fail:
+      - s_contains: "Unstable"
+    warn:
+      - s_contains: "Low-coverage"
+  perc:
+    pass:
+      - lt: 30.0
+    fail:
+      - gt: 30.0
+        eq: 30.0
+
+table_cond_formatting_colours:
+  - pass: "#2ecc71"
+  - fail: "#e74c3c"
+  - warn: "#f39c12"
+  - red: "#e74c3c"
+  - green: "#2ecc71"
+  - gray: "#3498db"
+
+msi_sensor_pro_coverage_threshold: 300
+msi_sensor_pro_min_sites: 10
+msi_high_threshold: 30
+
+custom_plot_config:
+  msi_summary:
+    defaultsort:
+      - column: "perc"
+        direction: desc
diff --git a/conf/modules.config b/conf/modules.config
@@ -352,6 +352,7 @@ process {
 
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+        container = 'my-multiqc:1.29-cmgg-dev'
     }
 }
 

diff --git a/docs/CITATIONS.md b/docs/CITATIONS.md
@@ -60,6 +60,9 @@
 
   > Brent S Pedersen, Aaron R Quinlan, Mosdepth: quick coverage calculation for genomes and exomes, Bioinformatics, Volume 34, Issue 5, 01 March 2018, Pages 867–868. doi: 10.1093/bioinformatics/btx699. PubMed PMID: 29096012. PubMed Central PMCID: PMC6030888.
 
+- [Msisensor-pro] (https://pubmed.ncbi.nlm.nih.gov/32171661/)
+  > Peng Jia, Xiaofei Yang, Li Guo, Bowen Liu, Jiadong Lin, Hao Liang, et al. MSIsensor-pro: fast, accurate, and matched-normal-sample-free detection of microsatellite instability. Genomics Proteomics Bioinformatics 2020.2020 Feb;18(1):65-71. doi: 10.1016/j.gpb.2020.02.001. Epub 2020 Mar 12. PubMed PMID: PMC7393535.
+
 - [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.

diff --git a/modules/nf-core/msisensorpro/pro/main.nf b/modules/nf-core/msisensorpro/pro/main.nf
diff --git a/workflows/smallvariants.nf b/workflows/smallvariants.nf
@@ -50,7 +50,7 @@ include { TABIX_TABIX as TABIX_TRUTH                                 } from '../
 include { BCFTOOLS_STATS as BCFTOOLS_STATS_FAMILY                    } from '../modules/nf-core/bcftools/stats/main'
 include { VCF2DB                                                     } from '../modules/nf-core/vcf2db/main'
 include { MULTIQC                                                    } from '../modules/nf-core/multiqc/main'
-include { MSISENSORPRO_PRO                                           } from '../modules/nf-core/msisensorpro/pro/main'  
+include { MSISENSORPRO_PRO                                           } from '../modules/nf-core/msisensorpro/pro/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -167,6 +167,7 @@ workflow SMALLVARIANTS {
 
     def ch_elsites            = elsites             ? Channel.fromPath(elsites).map{ elsites_file -> [[id:'elsites'], elsites_file] }.collect() : [[],[]]
 
+    def ch_msi_baseline       = Channel.fromPath(msi_baseline).map { msi_file -> [[id:"msi_baseline"], msi_file] }
     //
     // Check for the presence of EnsemblVEP plugins that use extra files
     //
@@ -446,26 +447,20 @@ workflow SMALLVARIANTS {
             cram: [meta, cram, crai, bed]
             bam: [meta, bam, bai, bed]
         }
-
-        //
-        // Check for MSI 
-        //
-    def ch_fasta_ready_broadcast = ch_caller_inputs.cram
-        .map { meta, _cram, _crai, _bed -> tuple(meta, file(params.fasta)) }
 
-    def ch_fai_ready_broadcast = ch_caller_inputs.cram
-        .map { meta, _cram, _crai, _bed -> tuple(meta, file(params.fai)) }
-    def ch_msi_baseline = ch_caller_inputs.cram.map { meta, _cram, _crai, _bed -> tuple(meta, file(msi_baseline)) }
+    //
+    // Check for MSI
+    //
+
     MSISENSORPRO_PRO(
-        ch_caller_inputs.cram.map { meta, cram, crai, _bed ->
-            tuple(meta, cram, crai) },
+        CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.ready_crams,
         ch_msi_baseline,
-        ch_fasta_ready_broadcast,
-        ch_fai_ready_broadcast
+        ch_fasta_ready,
+        ch_fai_ready
     )
     ch_reports  = ch_reports.mix(MSISENSORPRO_PRO.out.all_msi.map { _meta, file -> file})
-    ch_versions = ch_versions.mix(MSISENSORPRO_PRO.out.versions)
-
+    ch_reports  = ch_reports.mix(MSISENSORPRO_PRO.out.summary_msi.map { _meta, file -> file})
+    ch_versions = ch_versions.mix(MSISENSORPRO_PRO.out.versions.first())
 
     def ch_calls = Channel.empty()
     def ch_gvcf_reports = Channel.empty()
-Original file line number
+Diff line change
@@ Expand Up / @@ -352,6 +352,7 @@ process { @@
         withName: 'MULTIQC' {
             ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+            container = 'my-multiqc:1.29-cmgg-dev'
         }
     }
@@ Expand Down @@