Merge pull request #156 from nf-core/fix-help-1

Updates r packages & uses wave for container(s)

Author: atrigila

CHANGELOG.md

@@ -7,6 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- Addressed issues with latest GSVA function calls after GSVA >1.5.0 was introduced to be able to use gene score methods accordingly again
+- Updated the analysis dependencies in the local module for gene score computation to latest versions of the R Scripts
+- Removed container dependency on biocontainers and rather using Wave containers again
+
+### `Fixed`
+
 - [#151](https://github.com/nf-core/nanostring/pull/151) - Updated modules and subworkflows, and follow nextflow's strict syntax.
 
 ### `Changed`

modules/local/compute_gene_scores/environment.yml

@@ -2,12 +2,12 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::r-yaml=2.3.7
-  - conda-forge::r-ggplot2=3.4.4
+  - conda-forge::r-yaml=2.3.12
+  - conda-forge::r-ggplot2=4.0.1
   - conda-forge::r-dplyr=1.1.4
-  - conda-forge::r-stringr=1.5.0
-  - bioconda::bioconductor-gsva=1.46.0
-  - bioconda::bioconductor-singscore=1.18.0
-  - conda-forge::r-factominer=2.8.0
-  - conda-forge::r-tibble=3.2.1
-  - conda-forge::r-matrixstats=1.1.0
+  - conda-forge::r-stringr=1.6.0
+  - bioconda::bioconductor-gsva=2.0.0
+  - bioconda::bioconductor-singscore=1.26.0
+  - conda-forge::r-factominer=2.13.0
+  - conda-forge::r-tibble=3.3.1
+  - conda-forge::r-matrixstats=1.5.0

modules/local/compute_gene_scores/main.nf

@@ -2,9 +2,7 @@ process COMPUTE_GENE_SCORES {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-e6920e60d80922852a1b19630ebe16754cf5320d:75e2c0a29159bae8a964e43ae16a45c282fdf651-0' :
-        'biocontainers/mulled-v2-e6920e60d80922852a1b19630ebe16754cf5320d:75e2c0a29159bae8a964e43ae16a45c282fdf651-0' }"
+    container "community.wave.seqera.io/library/bioconductor-gsva_bioconductor-singscore_r-dplyr_r-factominer_pruned:e6f1a5cd9110d36b"
 
     input:
     tuple val(meta), path(normalized_counts)