update tbpipeline

Author: garcia-nacho

README.md

@@ -80,4 +80,4 @@ To remove TOP you must run <code>TOP.sh --uninstall</code>
 * Running TB-pipeline from trimmed fastq
 
 ## Under the hood   
-TOP is a Nextflow-based modular pipeline that used docker to isolate and run the different tools included in the analysis. The main TOP.sh is just a wrapper for the nextflow script (TOP.nf), with augmented functionalities such us update, and arguments passed to the nextflow script. The highly modular nature of TOP makes it easy to quickly add new analysis. You just need to add a process in the TOP.nf, include it in the workflow section of the TOP.nf and implement the parsing of the results into the output. The most straight forward to do it is by implementing it in the Summarizer.R script inside the Spades' docker image.     
+TOP is a modular Nextflow-based pipeline that use docker to isolate and run the different tools included in the analysis. The main TOP.sh is just a wrapper for the nextflow script (TOP.nf), with augmented functionalities such us update, uninsall and some arguments to be passed to the nextflow script. The highly modular nature of TOP makes it easy to quickly add new analysis. If you want to do it, you just need create or reuse a docker image with your tool of interest and to add a new process in the TOP.nf. Then, you call the process in the workflow section of the TOP.nf and implement the parsing of the resulting files into the output. The most straight forward to do it is by implementing it in the Summarizer.R script inside the Spades' docker image. After doing it, you can just      

TBpipeline/Scripts/TBCleaner.R

@@ -51,8 +51,9 @@ mykrobe$sample<-gsub("_.*","", mykrobe$sample)
 
 samples<-merge(samples.df, mykrobe, by.x = "samples", by.y = "sample")
 samples$Excluded<-"YES"
-if(length(which(samples$mash=="MTBC"))>0){
-  samples$Excluded[which(samples$mash=="MTBC")]<-"NO"
+
+if(length(which(samples$phylo_group=="Mycobacterium_tuberculosis_complex"))>0){
+  samples$Excluded[which(samples$phylo_group=="Mycobacterium_tuberculosis_complex")]<-"NO"
 }
 
 to.remove<-samples$dirs[which(samples$Excluded=="YES")]

TOP.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 source activate top_nf
-SHORT=u,r:,f:,h,t:,c:,d,s:,u
+SHORT=u,r:,f:,h,t:,c:,d,s:,x
 LONG=update,reads:,fastas:,help,tbdb:,cores:,dev,sp:,uninstall
 OPTS=$(getopt --options $SHORT --longoptions $LONG -- "$@")
 
@@ -29,7 +29,7 @@ do
       READS="$2"
       shift 2
       ;;
-    -u | --uninstall )
+    -x | --uninstall )
       echo "Removing TOP"
       rm ${TOPSHPATH}/TOP.sh
       conda deactivate top_nf
@@ -40,6 +40,29 @@ do
       echo "Running from fastas is not implemented yet"
       exit 2
       ;;
+    -u | --update )
+      echo "Updating The One Pipeline"
+      wget -O ${CONDA_PREFIX}/bin/TOP.nf https://github.com/garcia-nacho/TOP/raw/master/TOP.nf
+      wget -O ${CONDA_PREFIX}/bin/nextflow.config https://github.com/garcia-nacho/TOP/raw/master/nextflow.config
+      wget -O ${CONDA_PREFIX}/top_template.html https://github.com/garcia-nacho/TOP/raw/master/top_template.html
+      wget -O ${CONDA_PREFIX}/bin/TOP.sh https://github.com/garcia-nacho/TOP/raw/master/TOP.sh
+      
+      docker pull ghcr.io/garcia-nacho/top_spades
+      docker pull ghcr.io/garcia-nacho/top_abricate
+      docker pull ghcr.io/garcia-nacho/top_emmtyper
+      docker pull ghcr.io/garcia-nacho/top_hicap
+      docker pull ghcr.io/garcia-nacho/top_seroba
+      docker pull ghcr.io/garcia-nacho/top_virfinder
+      #docker pull ghcr.io/garcia-nacho/top_prokka
+      docker pull ghcr.io/garcia-nacho/top_ngstar
+      docker pull ghcr.io/garcia-nacho/top_tbpipeline
+      docker pull ghcr.io/garcia-nacho/top_seqsero
+      docker pull ghcr.io/garcia-nacho/top_ngmaster
+      docker pull ghcr.io/garcia-nacho/top_ecoli
+      docker pull ghcr.io/garcia-nacho/top_meningotype
+      docker pull ghcr.io/garcia-nacho/top_tartrate
+      exit 2
+      ;;
     -d | --dev )
       devmode=1
       shift
@@ -54,6 +77,8 @@ do
       echo "use -f or --fastas to run from a set of fastas e.g. TOP.sh -f /path/to/fastas"
       echo "use -d or --dev to run in development mode.(i.e all files are saved after a successful run)" 
       echo "use -h or --help to show this help" 
+      echo "use -u or --update to update the pipeline"
+      echo "use -x or --uninstall to uninstall the pipeline" 
       echo ""
       exit 2
       ;;
@@ -63,6 +88,7 @@ do
       ;;
     *)
       echo "Unexpected option: $1"
+      exit 2
       ;;
   esac
 done