From 81e851d5492551b636d8b55bc349d35cb9fbce1c Mon Sep 17 00:00:00 2001
From: Melvin Alappat <melvin.alappat@unibas.ch>
Date: Thu, 30 Dec 2021 14:26:45 +0100
Subject: [PATCH] feat: execution of python script in workflow
---
src/primingprob/PrimingProb_process.nf | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/src/primingprob/PrimingProb_process.nf b/src/primingprob/PrimingProb_process.nf
index 98f649c..59ba2a9 100644
--- a/src/primingprob/PrimingProb_process.nf
+++ b/src/primingprob/PrimingProb_process.nf
@@ -2,6 +2,7 @@
params.transcripts = "/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/transcript.fasta"
params.primers = "/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/primer.fasta"
+params.output = "/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/Potential_Priming_Sites.txt"
log.info """\
@@ -18,6 +19,8 @@ process RIblast_interaction {
path transcript from params.transcripts
path primer from params.primers
+ output:
+ file "Energies.txt" into energy_channel
script:
"""
@@ -27,6 +30,24 @@ process RIblast_interaction {
}
+process PrimingProb {
+
+ input:
+ file energy from energy_channel
+ path transcript from params.transcripts
+ path output from params.output
+
+ script:
+ """
+
+ cli_priming_prob.py $energy $transcript $output
+
+ """
+
+
+}
+
+
--
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