Moved ChromHMM executable to bin

daisybio · Dec 13, 2023 · 39e3df9 · 39e3df9
1 parent 95a1d91
commit 39e3df9
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Showing 3 changed files with 2 additions and 2 deletions.
diff --git a/assets/chromhmm/ChromHMM.jar → bin/ChromHMM.jar b/assets/chromhmm/ChromHMM.jar → bin/ChromHMM.jar
diff --git a/modules/local/chromhmm/binarize_bams.nf b/modules/local/chromhmm/binarize_bams.nf
@@ -13,7 +13,7 @@ process BINARIZE_BAMS {
 
     script:
     """
-	java -jar ${projectDir}/assets/ChromHMM.jar BinarizeBam \
+	java -jar ChromHMM.jar BinarizeBam \
 		$chromsizes \
 		reformatted_bams \
 		$cellmarkfiletable \

diff --git a/modules/local/chromhmm/learn_model.nf b/modules/local/chromhmm/learn_model.nf
@@ -15,7 +15,7 @@ process LEARN_MODEL {
     """
 	// Organism (PLACEHOLDER) only needed for downstream analysis of ChromHMM and therefore not supplied
 
-	java -jar ${projectDir}/assets/ChromHMM.jar LearnModel \
+	java -jar ChromHMM.jar LearnModel \
         -p $task.cpus \
 		$binarized_bams \
 		ChromHMM_output \