Change: Limit mldm runtime and remove iteration increment code

segrelab · Nov 17, 2021 · 789f030 · 789f030
1 parent 0a17ca2
commit 789f030
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Showing 2 changed files with 2 additions and 8 deletions.
diff --git a/micone/pipelines/configs/process.config b/micone/pipelines/configs/process.config
@@ -21,6 +21,7 @@ process {
     }
     withLabel: 'mldm' {
         conda = "${params.conda_dir}/micone-mldm"
+        time = '4hours'
     }
     withLabel: 'cozine' {
         conda = "${params.conda_dir}/micone-cozine"

diff --git a/micone/pipelines/templates/network_inference/direct/mldm.R b/micone/pipelines/templates/network_inference/direct/mldm.R
@@ -35,14 +35,7 @@ sample.md <- read_sample_data(sample_metadata) # Must be purely numeric or categ
 
 mldmNetwork <- mLDM(X=otu_t, M=sample.md, Z_mean=Z_mean, max_iteration=max_iteration, verbose=TRUE)
 
-optimal <- mldmNetwork\$optimal
-if (length(optimal) > 0) {
-    otuNetwork <- mldmNetwork\$optimal[[9]]
-} else {
-    new_max_iteration <- max_iteration * 10
-    mldmNetwork <- mLDM(X=otu_t, M=sample.md, Z_mean=Z_mean, max_iteration=new_max_iteration, verbose=TRUE)
-    otuNetwork <- mldmNetwork\$optimal[[9]]
-}
+otuNetwork <- mldmNetwork\$optimal[[9]]
 
 rownames(otuNetwork) <- rownames(otu)
 colnames(otuNetwork) <- rownames(otu)