Running with multiple inputs about squire HOT 6 OPEN

Hope it works now! Cheers!

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Hi!
Have you checked the loop_map.sh script? In there, you'll see an example of running squire Map for multiple inputs. Basically, it runs squire Map in a for loop.
Cheers!

from squire.

Thanks for pointing me to this script! So to clarify, running squire Map with multiple inputs (e.g. squire Map -1 input1_1,input2_1,input3_1 -2 input1_2,input2_2,input3_2...) does not merge the multiple inputs in any way, but instead runs squire Map on each input sequentially?

from squire.

Actually, it should work if you separate the input files with commas. You can try and run your line of code, but without specifying sample name with --name, so it "uses basename of read1 as default" as specified in Map.py

from squire.

I did separate the input files with commas when I ran it (as written above, squire Map -1 input1_1,input2_1,input3_1) but I think you are right that it may have been the "--name" flag that caused there to be only one output. I will try running it again without this flag. Thanks!!

from squire.

Hi! Have you checked the loop_map.sh script? In there, you'll see an example of running squire Map for multiple inputs. Basically, it runs squire Map in a for loop. Cheers!

@rpg18
I've tried running the loop_map.sh script, because I have multiple samples. But it gives me the following error (described here: #72 (comment)). It basically concatenates the path to the files from my first sample with the path to the files from to my second sample and therefore gives me an error. Have you run loop_map.sh successfully with multiple samples? If so, how did you fix this issue?

Thank you!

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