Issue with Polca input

[asan-emirsaleh]

Great job! I planned to use this EC tool too. The error I faced was in that Polca expected fastq files to be gzipped.

gzip: $SR1.gz: No such file or directory
gzip: $SR2.gz: No such file or directory

[asan-emirsaleh]

After I have defined the full path to fastq.gz files polca started to process assembly.

[gunjanpandey]

This is a major issue as polca refuses to parse variables. Please tell how to parse $R1 and $R1 variables in the -r flag of polca.

polca.sh -a "$input_file" -r '$R1 $R2' -t "$CORES" -m 6G

I have tried many ways, including double quotes and methods described here https://stackoverflow.com/questions/13799789/expansion-of-variables-inside-single-quotes-in-a-command-in-bash