Merge pull request #144 from WackerO/control_features_fix

Fix control_features and sizefactors_from_controls

CHANGELOG.md

@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#116](https://github.com/nf-core/differentialabundance/issues/116)] - Skip outlier detection with low replication ([@pinin4fjords](https://github.com/pinin4fjords), review by [@nvnieuwk](https://github.com/nvnieuwk))
 - [[#122](https://github.com/nf-core/differentialabundance/pull/126)] - Add spaces to satisfy nf-core download for singularity ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#127](https://github.com/nf-core/differentialabundance/issues/127)] - [Bug] Can't pass samplesheet with -c file.config , or -params-file params.yml or directly with --input samplesheet.csv ([@ctuni](https://github.com/ctuni), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#138 ](https://github.com/nf-core/differentialabundance/issues/138)]- Fix bugs with --control_features and --sizefactors_from_controls ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 
 ## v1.2.0 - 2023-04-19
 

nextflow.config

@@ -17,7 +17,7 @@ params {
     contrasts                  = null
     matrix                     = null
     control_features           = null
-    sizefactors_from_controls  = null
+    sizefactors_from_controls  = false
 
     // Reporting
     logo_file                  = "${projectDir}/docs/images/nf-core-differentialabundance_logo_light.png"

workflows/differentialabundance.nf

@@ -35,7 +35,7 @@ if (params.study_type == 'affy_array'){
 }
 
 // Check optional parameters
-if (params.control_features) { ch_control_features = file(params.control_features, checkIfExists: true) } else { ch_control_features = [[],[]] }
+if (params.control_features) { ch_control_features = Channel.of([ exp_meta, file(params.control_features, checkIfExists: true)]).first() } else { ch_control_features = [[],[]] }
 if (params.gsea_run) {
     if (params.gsea_gene_sets){
         gene_sets_files = params.gsea_gene_sets.split(",")