update deeptools version and template nextflow

.gitignore

@@ -22,4 +22,4 @@ nextflow
 .nextflow.log*
 .nextflow/
 work/
-results
+results*

src/RNAseq.config

@@ -194,7 +194,7 @@ profiles {
         cpus = 1
       }
       withName: coverage_genome {
-        container = "lbmc/deeptools:3.0.2"
+        container = "lbmc/deeptools:3.1.1"
         cpus = 8
       }
     }

src/nextflow_template.sh

@@ -3,16 +3,16 @@
 set -e
 
 nextflow src/RNAseq.nf -c src/RNAseq.config \
-                       -profile psmn\
+                       -profile docker\
                        -resume\
                        --do_fastqc true\
-                       --do_dedup true\
+                       --do_dedup false\
                        --do_postgenome true\
                        --adaptorR1 "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"\
                        --adaptorR2 "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"\
                        --strand "FR"\
-                       --fastq_raw "data/fastq/*{_R1,_R2}_short.fastq.gz"\
-                       --output "results"\
+                       --fastq_raw "data/fastq/*HIV1*{_R1,_R2}_short.fastq.gz"\
+                       --output "results_tophatVShisat/tophat"\
                        --filter "data/filter/*.bt2"\
                        --index_genome "data/genome/*.ht2"\
                        --gtf "data/annotation/gencode.v28.annotation_v3.gtf"\