Dev report

• Renommage de beaucoup de variables et de channels
• Suppression des appels à Rscript avec le chemin absolu des scripts
• Concaténation du rapport final à la fin
• Suppression des chemins absolus dans le dev/test.config

bin/Nremove.sh

@@ -19,7 +19,7 @@ input_file=$1
 output_file=$2
 log=$3
 
-echo -e "<br /><br />\n\n### Removal for reads made of N only\n\n" >> ${log}
+echo -e "<br /><br />\n\n### Removal for reads made of N only\n\n" > ${log}
 zcat ${input_file} | awk '{lineKind=(NR-1)%4;}lineKind==0{record=$0; next}lineKind==1{toGet=!($0~/^N*$/); if(toGet) print record}toGet' | gzip -c > ${output_file}
 # warning: with no output dir for log.txt, the file is created in \\wsl$\Ubuntu-20.04\home\gael\work\35\b826898b7be994ff13b7bc73bc88d8\
 # get the bad sequences + 3 other lines of the fastq #see https://stackoverflow.com/questions/11793942/delete-lines-before-and-after-a-match-in-bash-with-sed-or-awk