Chaning for deployment and typos

.gitignore

@@ -23,4 +23,9 @@ RNAz-2.1
 **/uploads/**
 **/reports/**
 **/nextjs/public/example/scoelicolor/report/**
-**/nextjs/public/example/bacteroides/report/**
+**/nextjs/public/example/scoelicolor/report_old/**
+**/nextjs/public/example/cjejuni/report/**
+**/nextjs/public/example/cjejuni/report_old/**
+**/nextjs/public/example/bacteroidesplasmid/report_old/**
+**/nextjs/public/example/bacteroidesplasmid/report/**
+**/nextjs/public/example/cjejuni/report/**

nf/bin/templates/overview.html

@@ -12,9 +12,9 @@ <h1 class="h3 mb-0 text-gray-800">Overview of data</h1>
     For the more information on the tools and parameters used in TSS-CAPTUR, please refer to the <a href="references.html">references</a>.
 </p> 
 <p class="mb-4">The current page presents an overview of the results of all steps run in TSS-CAPTUR, for example, the length of the transcript originally extracted from the genome and the predicted classification. 
-    In the case of RNA-transcripts, a terminator might have been allocated to the transcript and the coordinates would have been adapted. 
-    Also, a secondary structure analysis is run using <a href="https://academic.oup.com/nar/article/36/suppl_2/W70/2505776">RNAFold</a> RNA transcripts and allows a visualization of it.
-    All transcript undergo a motif analysis of the promoter region using <a href="https://doi.org/10.1093/nar/gkp335">MEME</a> A short descriptive overview follows:
+    Moreover, a terminator might have been allocated to the transcript and the length of the transcript would have been adapted. 
+    Also, a secondary structure analysis is run using <a href="https://academic.oup.com/nar/article/36/suppl_2/W70/2505776">RNAFold</a> for the transcripts, providing a visualization of its structure.
+    All transcript undergo a motif analysis of the promoter region using <a href="https://doi.org/10.1093/nar/gkp335">MEME</a>. A short descriptive overview follows:
 </p>
 <div class="row">
 

nf/nextflow.config

@@ -3,8 +3,8 @@ includeConfig "conf/params.config"
 
 process.cpus = 4
 
-docker {
-    process.container = "mwittep/tsscaptur:v2"
-    runOptions = "--mount  type=bind,src=$params.BLASTDB,target=/tmp"
-    docker.enabled = true
-}
+// docker {
+//    process.container = "mwittep/tsscaptur:v2"
+//    runOptions = "--mount  type=bind,src=$params.BLASTDB,target=/tmp"
+//    docker.enabled = true
+// }