Added -n option to ivar consensus. Adde nano, vim and pandas to Docke…

…rfile.

Dockerfile

@@ -2,7 +2,7 @@ FROM ubuntu:18.04
 MAINTAINER Karthik G <[email protected]>
 
 RUN apt-get update
-RUN apt-get install -y build-essential autoconf zlib1g-dev python3 wget libbz2-dev liblzma-dev libncurses-dev git bedtools python3-pip
+RUN apt-get install -y build-essential autoconf zlib1g-dev python3 wget libbz2-dev liblzma-dev libncurses-dev git bedtools python3-pip vim nano
 # HTSlib
 RUN cd root/ &&\
     wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 &&\
@@ -42,4 +42,4 @@ RUN cd root/ &&\
     rm v0.7.17.tar.gz
 ENV PATH /root/bwa-0.7.17:$PATH
 # Snakemake
-RUN pip3 install snakemake
+RUN pip3 install pandas snakemake

pipeline_consensus/Snakefile

@@ -31,7 +31,7 @@ rule call_consensus:
         "{out_dir}/consensus_sequences/{sample}.fa"
     shell:
         """
-        samtools mpileup -A -Q 0 -d 300000 {input} | ivar consensus -p {output} -m 10
+        samtools mpileup -A -Q 0 -d 300000 {input} | ivar consensus -p {output} -m 10 -n N
         """
 
 rule trim_reads: