Update viber module

modules/nf-core/viber/environment.yml

@@ -3,7 +3,7 @@ channels:
   - bioconda
 
 dependencies:
-  - bioconda::r-cnaqc=1.1.2
+  - bioconda::r-cnaqc=1.1.3
   - bioconda::r-viber=1.0.0
   - conda-forge::r-cli=3.6.5
   - conda-forge::r-dplyr=1.1.4

modules/nf-core/viber/main.nf

@@ -4,8 +4,8 @@ process VIBER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/r-cnaqc_r-viber:014077a3164189d5':
-        'community.wave.seqera.io/library/r-cnaqc_r-viber:2314592f7d2f9abe'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/21/21e21fc0c84576a262f02779cb091dbe2734a12e3b9a2c41e08cb8393bd3953f/data':
+        'community.wave.seqera.io/library/r-cnaqc_r-viber_r-cli_r-dplyr_pruned:f00a3b14d68a7bac'}"
 
     input:
     tuple val(meta), path(rds_join), val(tumour_samples)

modules/nf-core/viber/templates/viber_main_script.R

@@ -1,5 +1,7 @@
 #!/usr/bin/env Rscript
 
+options(easypar.parallel=FALSE)
+
 parse_args = function(x) {
     x = gsub("\\\\[","",x)
     x = gsub("\\\\]","",x)
@@ -37,22 +39,25 @@ library(ggpubr)
 
 samples = substr("$tumour_samples", 2, nchar("$tumour_samples")-1)
 samples = strsplit(samples, ", ")[[1]]
-print("$meta.patient")
-print("$tumour_samples")
-print("$rds_join")
-print(samples)
+
+cli::cli_text("Patient $meta.patient with samples $tumour_samples.")
+cli::cli_text("Input file: $rds_join.")
 
 if ( grepl(".rds\$", tolower("$rds_join")) ) {
     input_obj = readRDS("$rds_join")
     if (class(input_obj) == "m_cnaqc") {
         shared = input_obj %>% get_sample(sample=samples, which_obj="shared")
         joint_table = lapply(names(shared),
-                        function(sample_name)
-                        shared[[sample_name]] %>%
-                            CNAqc::subset_by_segment_karyotype("1:1") %>%
-                            CNAqc::Mutations() %>%
-                            dplyr::mutate(sample_id=sample_name)
-                        ) %>% dplyr::bind_rows()
+                        function(sample_name) {
+                          table_s = shared[[sample_name]] %>%
+                              CNAqc::subset_by_segment_karyotype("1:1") %>%
+                              CNAqc::Mutations() %>%
+                              dplyr::mutate(sample_id=sample_name)
+                          if (nrow(table_s) == 0) {
+                            cli::cli_alert_warning("Sample {sample_name} has no diploid mutations!")
+                          }
+                          return(table_s)
+                        }) %>% dplyr::bind_rows()
         } else {
           cli::cli_alert_warning("Object of class {class(input_obj)} not supported.")
           return()
@@ -61,7 +66,11 @@ if ( grepl(".rds\$", tolower("$rds_join")) ) {
   joint_table = read.csv("$rds_join")
 }
 
-print("Subset joint done")
+if (nrow(joint_table) == 0) {
+  cli::cli_alert_warning("No samples contain diploid mutations!")
+}
+
+cli::cli_text("Joint table created.")
 
 ## Read input joint table
 input_tab = joint_table %>%
@@ -88,12 +97,12 @@ nv = reads_data %>%
 # Standard fit
 viber_K = as.integer(opt[["K"]])
 
-message("Starting standard fit")
+cli::cli_text("Starting standard fit")
 st_fit = VIBER::variational_fit(nv, dp,
                                 K=viber_K,
                                 data=reads_data)
 st_fit[["description"]]="$meta.patient"
-message("End standard fit")
+cli::cli_text("End standard fit")
 best_fit = best_fit_heuristic = st_fit
 
 # If all clusters are removed -> keep the origianl best fit

modules/nf-core/viber/tests/main.nf.test.snap

@@ -2,14 +2,14 @@
     "viber - csv": {
         "content": [
             [
-                "versions.yml:md5,d27db9579ed0b91c5131d11f037ec121"
+                "versions.yml:md5,0aff4c2ae3de260cbef5870e5f4f0374"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-10-10T17:31:00.066038"
+        "timestamp": "2026-01-21T18:29:55.951523"
     },
     "viber - csv - stub": {
         "content": [
@@ -171,14 +171,14 @@
     "viber - rds": {
         "content": [
             [
-                "versions.yml:md5,d27db9579ed0b91c5131d11f037ec121"
+                "versions.yml:md5,0aff4c2ae3de260cbef5870e5f4f0374"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-10-10T17:27:18.630026"
+        "timestamp": "2026-01-21T18:34:41.655887"
     },
     "viber - rds - stub": {
         "content": [