I have downloaded and installed the Biostars Bioinformatics-recipes according to the directions here: https://bioinformatics-recipes.readthedocs.io/en/latest/index.html

OS = Ubuntu 18, anaconda python

I am unable to get a simple script to work.

I created a new project -> uploaded a data file (filelist.txt) which is a text file just listing the full path to some files

The data tab shows:
Data:filelist.txt

Data List

Files contained in the dataset

filelist.txt

Data Content

/home/test/biorecipes/trimFastq/Y12_R1.fastq

/home/test/biorecipes/trimFastq/Y12_R2.fastq

Table of Contents filelist.txt

Then I added a data field to the recipe: [data]

label = 'Pick data'

source = 'PROJECT'

help = 'Pick data from this project.'

choices = [ ['A','Default'] ]

This allows me to choose my filelist.txt on the run tab.

In the code tab I have:

echo 'List my files'

echo $PWD

cat filelist.txt

When I run I get the following error:

cat: filelist.txt: No such file or directory

Command 'bash recipe.sh' returned non-zero exit status 1.

when I run only:

echo 'List my files'

echo $PWD

I get the expected result.

Suggestions would be helpful.

Thank you