Merge remote-tracking branch 'origin/dev' into dev

bigbio · May 1, 2022 · 2626e22 · 2626e22
2 parents 6686fa2 + 280dd6d
commit 2626e22
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Showing 2 changed files with 1 addition and 2 deletions.
diff --git a/bin/msstats_plfq.R b/bin/msstats_plfq.R
@@ -202,7 +202,6 @@ if (l == 1) {
     contrast_mat <- parse_contrasts(l = l, contrast_str = contrast_str, lvls = lvls)
     print ("Contrasts to be tested:")
     print (contrast_mat)
-    #TODO allow for user specified contrasts
     test.MSstats <- groupComparison(contrast.matrix=contrast_mat, data=processed.quant)
 
     mic <- get_missing_in_condition(processed.quant$ProteinLevelData)

diff --git a/modules/local/msstats/main.nf b/modules/local/msstats/main.nf
@@ -1,7 +1,7 @@
 process MSSTATS {
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bioconductor-msstats=4.2.0 conda-forge::r-here" : null)
+    conda (params.enable_conda ? "bioconda::bioconductor-msstats=4.2.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/bioconductor-msstats:4.2.0--r41h619a076_1"
     } else {