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
@@ -37,3 +37,36 @@ mosdepth_config:
     - "HLA*"
     - "chrM"
     - "chrEBV"
+
+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/assets/samplesheet.csv b/assets/samplesheet.csv
@@ -1,4 +1,4 @@
-sample,family,cram,crai,roi,truth_vcf,truth_tbi,truth_bed,vardict_min_af
-NA24143,Proband_12.345,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/crams/NA24143.cram,,,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/vcfs/NA24143.vcf.gz,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/vcfs/NA24143.vcf.gz.tbi,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/regions/roi.bed,0.01
-NA24149,Proband_12.345,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/crams/NA24149.cram,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/crams/NA24149.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/regions/roi.bed,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/vcfs/NA24149.vcf.gz,,,
-NA24385,Proband_12.345,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/crams/NA24385.cram,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/crams/NA24385.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/regions/roi.bed,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/vcfs/NA24385.vcf.gz,,,
+sample,family,cram,crai,roi,truth_vcf,truth_tbi,truth_bed,vardict_min_af,msi
+NA24143,Proband_12.345,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/crams/NA24143.cram,,,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/vcfs/NA24143.vcf.gz,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/vcfs/NA24143.vcf.gz.tbi,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/regions/roi.bed,0.01,false
+NA24149,Proband_12.345,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/crams/NA24149.cram,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/crams/NA24149.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/regions/roi.bed,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/vcfs/NA24149.vcf.gz,,,,true
+NA24385,Proband_12.345,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/crams/NA24385.cram,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/crams/NA24385.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/regions/roi.bed,https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/illumina/vcfs/NA24385.vcf.gz,,,,false
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -112,6 +112,11 @@
             "vardict_min_af": {
                 "type": "number",
                 "meta": ["vardict_min_af"]
+            },
+            "msi": {
+                "type": "boolean",
+                "default": false,
+                "meta": "msi"
             }
         },
         "required": ["sample"]

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 = 'quay.io/cmgg/multiqc_cmgg:0.0.3dev'
     }
 }
 

diff --git a/docs/CITATIONS.md b/docs/CITATIONS.md
@@ -60,6 +60,10 @@
 
   > 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/main.nf b/main.nf
@@ -166,6 +166,7 @@ workflow {
         params.outdir,
         GlobalVariables.pedFiles,
         params.elsites,
+        params.msi_baseline,
 
         // Boolean inputs
         params.dragstr,

diff --git a/modules.json b/modules.json
@@ -129,6 +129,12 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/mosdepth/mosdepth.diff"
                     },
+                    "msisensorpro/pro": {
+                        "branch": "master",
+                        "git_sha": "fafa7b3a577412b6bde309170408da4cb911f04b",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/msisensorpro/pro/msisensorpro-pro.diff"
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",

diff --git a/modules/nf-core/msisensorpro/pro/environment.yml b/modules/nf-core/msisensorpro/pro/environment.yml
diff --git a/modules/nf-core/msisensorpro/pro/main.nf b/modules/nf-core/msisensorpro/pro/main.nf
diff --git a/modules/nf-core/msisensorpro/pro/meta.yml b/modules/nf-core/msisensorpro/pro/meta.yml
diff --git a/modules/nf-core/msisensorpro/pro/msisensorpro-pro.diff b/modules/nf-core/msisensorpro/pro/msisensorpro-pro.diff
-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 = 'quay.io/cmgg/multiqc_cmgg:0.0.3dev'
         }
     }
@@ Expand Down @@