Include folder in make.file output 1.41.1

When I put make.file command, I get back the following in the stability.files

Gp3wk41.Gp3wk41 Gp3wk41.Gp3wk41_S58_L001_R1_001.fastq.gz Gp3wk41.Gp3wk41_S58_L001_R2_001.fastq.gz

I want
Gp3wk41.Gp3wk41 fastq/Gp3wk41.Gp3wk41_S58_L001_R1_001.fastq.gz fastq/Gp3wk41.Gp3wk41_S58_L001_R2_001.fastq.gz

Hi - can you provide the syntax of the make.file command you are running?

Hey Pat

I realized that we needed to include inputdir in the make.contigs as well as make.file. All is well now!

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