add src/nextflow_template.sh

src/nextflow_template.sh

+#! /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"