Hi,
A small bug, but I when I had 30 paired end fastqs named NNNX1 through NNNX30 (with both "_1" and "_2" suffixes) in the raw data folder and I only listed X1 through X6 in my .csv file the script started working on NNNX10 and NNNX11, and then continued with NNNX12. I am assumed that the fastq file names in the CSV need to be unique and not nested in one another. I am guessing that a pattern match of NNNX1 matched all of the other fastq file names as well.
My work around was to make NNNX1 through NNNX3 non-unique by adding an "A" at the end of these file names, so that the paired end files could be uniquely paired.
Ran using docker.
Reed
Hi,
A small bug, but I when I had 30 paired end fastqs named NNNX1 through NNNX30 (with both "_1" and "_2" suffixes) in the raw data folder and I only listed X1 through X6 in my .csv file the script started working on NNNX10 and NNNX11, and then continued with NNNX12. I am assumed that the fastq file names in the CSV need to be unique and not nested in one another. I am guessing that a pattern match of NNNX1 matched all of the other fastq file names as well.
My work around was to make NNNX1 through NNNX3 non-unique by adding an "A" at the end of these file names, so that the paired end files could be uniquely paired.
Ran using docker.
Reed