fix qdnaseq env

Author: nvnieuwk

modules/local/qdnaseq/environment.yml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bioconductor-qdnaseq=1.42.0
+  - conda-forge::r-base=4.4.3
+  - conda-forge::r-lsr=0.5.2

modules/local/qdnaseq/main.nf

@@ -2,7 +2,10 @@ process QDNASEQ {
     tag "$meta.id"
     label 'process_low'
 
-    container "quay.io/cmgg/qdnaseq:0.0.4"
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/77/77b057272e6af69070dc1ee73d0a39d144e6641c0f4e625673de979b21b7bfd0/data':
+        'community.wave.seqera.io/library/bioconductor-qdnaseq_r-base_r-lsr:0304e1e0cbed3eab' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -13,7 +16,7 @@ process QDNASEQ {
     tuple val(meta), path("*.cna")              , emit: cna
     tuple val(meta), path("*_segments.txt")     , emit: segments
     tuple val(meta), path("statistics.out")     , emit: statistics
-    path "versions.yml"                         , emit: versions
+    path "versions.yml"                         , emit: versions, topic: versions
 
     script:
     template "qDNAseq.R"

modules/local/qdnaseq/templates/qDNAseq.R

@@ -122,8 +122,12 @@ write.table(std, file="statistics.out", append = TRUE, col.names = FALSE, row.na
 write.table(mad, file="statistics.out", append = TRUE, col.names = FALSE, row.names=c("mad"), dec = ",")
 write.table(aad, file="statistics.out", append = TRUE, col.names = FALSE, row.names=c("aad"), dec = ",")
 
-
-sink("versions.yml")
-cat("\\"task.process\\":\n")
-cat("    bioconductor-qdnaseq: 1.34.0\n")
-cat("    r-lsr: 0.5.2\n")
+## VERSIONS FILE
+writeLines(
+    c(
+        '"${task.process}":',
+        paste('    r-base:', strsplit(version[['version.string']], ' ')[[1]][3]),
+        paste('    r-lsr:', as.character(packageVersion('lsr'))),
+        paste('    bioconductor-qdnaseq:', as.character(packageVersion('QDNAseq')))
+    ),
+'versions.yml')

subworkflows/local/bam_variant_calling_qdnaseq/main.nf

@@ -45,13 +45,11 @@ workflow BAM_VARIANT_CALLING_QDNASEQ {
         ch_qdnaseq_input.male,
         ch_qdnaseq_male
     )
-    ch_versions = ch_versions.mix(QDNASEQ_MALE.out.versions.first())
 
     QDNASEQ_FEMALE(
         ch_qdnaseq_input.female,
         ch_qdnaseq_female
     )
-    ch_versions = ch_versions.mix(QDNASEQ_FEMALE.out.versions.first())
 
     def ch_qdnaseq_beds = QDNASEQ_MALE.out.bed
         .mix(QDNASEQ_FEMALE.out.bed)

tests/default.nf.test.snap

@@ -46,6 +46,16 @@
                 "PREPROCESS_GTF": {
                     "grep": 3.11
                 },
+                "QDNASEQ_FEMALE": {
+                    "r-base": "4.4.3",
+                    "r-lsr": "0.5.2",
+                    "bioconductor-qdnaseq": "1.42.0"
+                },
+                "QDNASEQ_MALE": {
+                    "r-base": "4.4.3",
+                    "r-lsr": "0.5.2",
+                    "bioconductor-qdnaseq": "1.42.0"
+                },
                 "SAMTOOLS_CONVERT": {
                     "samtools": "1.22.1"
                 },
@@ -64,10 +74,6 @@
                 },
                 "Workflow": {
                     "nf-cmgg/structural": "v0.3.0"
-                },
-                "task.process": {
-                    "bioconductor-qdnaseq": "1.34.0",
-                    "r-lsr": "0.5.2"
                 }
             },
             [
@@ -208,6 +214,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-13T14:11:41.354981093"
+        "timestamp": "2026-01-13T15:21:35.911930138"
     }
 }