add template for Riboseq

src/nextflow_template.sh

@@ -2,6 +2,7 @@
 
 set -e
 
+# For RNASeq
 nextflow src/RNAseq.nf -c src/RNAseq.config \
                        -profile docker\
                        -resume\
@@ -11,8 +12,25 @@ nextflow src/RNAseq.nf -c src/RNAseq.config \
                        --adaptorR1 "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"\
                        --adaptorR2 "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"\
                        --strand "FR"\
-                       --fastq_raw "data/fastq/*HIV1*{_R1,_R2}_short.fastq.gz"\
-                       --output "results_tophatVShisat/tophat"\
+                       --fastq_raw "data/fastq/*{_R1,_R2}_short.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"
+
+# For Ribosome Profiling
+nextflow src/RibosomeProfiling.nf -c src/RNAseq.config \
+                       -profile docker\
+                       -resume\
+                       --do_fastqc true\
+                       --do_dedup false\
+                       --do_postgenome true\
+                       --adaptorR1 "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"\
+                       --strand "F"\
+                       --fastq_raw "data/fastq/*.fastq.gz"\
+                       --output "results"\
                        --filter "data/filter/*.bt2"\
                        --index_genome "data/genome/*.ht2"\
                        --gtf "data/annotation/gencode.v28.annotation_v3.gtf"\