change config

hnnd · Sep 27, 2020 · 281f602 · 281f602
1 parent a9f6429
commit 281f602
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Showing 3 changed files with 10 additions and 3 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -1,2 +1,8 @@
-process.container = 'nextflow/rnaseq-nf'
-docker.runOptions='-u $(id -u):$(id -g)'
+//process.container = 'nextflow/rnaseq-nf'
+//docker.runOptions='-u $(id -u):$(id -g)'
+//docker.enabled = true
+process {
+  executor='sge'
+}
+process.clusterOptions = '-S /bin/bash' 
+env.PATH="/opt/miniconda3/envs/nf/bin:$PATH"
diff --git a/script2.nf b/script2.nf
@@ -33,4 +33,4 @@ process index {
     salmon index --threads $task.cpus -t $transcriptome -i index
     """
 }
-
+index_ch.view() 
diff --git a/script3.nf b/script3.nf
@@ -17,3 +17,4 @@ log.info """\
 
 
 read_pairs_ch = Channel .fromFilePairs(params.reads)
+read_pairs_ch.view()
-Original file line number
+Diff line change
@@ Expand Up / @@ -33,4 +33,4 @@ process index { @@
         salmon index --threads $task.cpus -t $transcriptome -i index
         """
     }
+    index_ch.view()
Original file line number	Diff line number	Diff line change
Expand Up		@@ -17,3 +17,4 @@ log.info """\


		read_pairs_ch = Channel .fromFilePairs(params.reads)
		read_pairs_ch.view()