Mtoolbox.sh, issue with large number of samples

mitoNGS / MToolBox

A bioinformatics pipeline to analyze mtDNA from NGS data

GNU General Public License v3.0

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Closed psterk closed 5 years ago

psterk commented 5 years ago

The following line of code fails silently when the argument line becomes too long for ls:

if [[ ls -1 OUT*/*annotation.csv 2> /dev/null | wc -l -gt 0 ]]

This can be fixed by using find/xargs instead of ls:

if [[ find OUT* -name "*annotation.csv" 2> /dev/null | wc -l -gt 0 ]]

Same with two occurrences of:

for i in $(ls -d OUT_/ annotation.csv)

Can be fixed as follows:

for i in $(find OUT_/ -name "annotation.csv")

clody23 commented 5 years ago

Hi, thank you. Very well spotted! We have incorporated the fix you suggested.

Best, Claudia