From 8107d92fedeed23b89c5cb0d61689dd4a9270dab Mon Sep 17 00:00:00 2001
From: Emmanuel Labaronne <emmanuel.labaronne@ens-lyon.fr>
Date: Mon, 28 Sep 2020 14:20:44 +0200
Subject: [PATCH] add src/nextflow_template.sh
---
src/nextflow_template.sh | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
create mode 100644 src/nextflow_template.sh
diff --git a/src/nextflow_template.sh b/src/nextflow_template.sh
new file mode 100644
index 00000000..d37a8de6
--- /dev/null
+++ b/src/nextflow_template.sh
@@ -0,0 +1,20 @@
+#! /bin/bash
+
+set -e
+
+nextflow src/RNAseq.nf -c src/RNAseq.config \
+ -profile docker\
+ -resume\
+ --do_fastqc true\
+ --do_dedup true\
+ --do_postgenome true\
+ --adaptorR1 = "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"\
+ --adaptorR2 = "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"\
+ --strand = "FR"\
+ --fastq_raw "data/fastq/*{_R1,_R2}.fastq.gz"\
+ --output "results"\
+ --filter "data/filter/*.bt2"\
+ --index_genome "data/genome/*.ht2"\
+ --gtf "data/annotation/gencode.v28.annotation_v3.gtf"\
+ --gtf_collapse "data/annotation/gencode.v28.annotation_v3_collapse.gtf"\
+ --index_postgenome "data/post_genome/*.ht2"
--
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