Re: combine parallel with mocat structur

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Luis Pedro Coelho

Dec 14, 2020, 12:35:03 AM12/14/20
to Ulrike Löber, NGLess List

samples = readlines('samplelist.txt')

samples is going to be a list of strings (NGList NGLString—arguably not a very clear notation) because that's what readlines returns

current = lock1(samples)

current is a string (one of its inputs)

#input = paired("data/" + current + ".1.fq.gz", "data/" + current + ".2.fq.gz")
input = load_mocat_sample(samples)

You probably meant to write

input = load_mocat_sample(sample)

(no s at the end)

In more recent NGLess versions, you can use

input = load_fastq_directory(sample)

and it's the same thing (we have now extended MOCAT's structure too so that every MOCAT directory works with NGLess, but the converse is not true: NGLess is more flexible in naming convention and supports more compression formats).


I need to process ~200 samples with different numbers of input fastqs due to sequencing issues. My approach would be to create a mocat like structure having one folder for each sample with the different input fastqs stored in these directories. However, the syntax I used does not work. Is this the way to go, or is there even a better way, and what do I need to change in my script?
Thanks in advance!

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