How to adapt a for loop of `muscle` alignments using GNU Parallel?

How to adapt a for loop of `muscle` alignments using GNU Parallel?

0

I’m trying to adapt the following lines of code for use with GNU parallel:

for ID in $(cut -f1 markers.tsv);
    do echo $ID;
    FAA=${ID}.faa.gz
    zcat ${FAA} | muscle -out ${ID}.msa
    done

However, the examples I’m seeing here do not show where I can use my ${ID} argument.

Can someone help me adapt this using --jobs 16?

This could be one a one liner:

for ID in $(cut -f1 markers.tsv);
    do echo $ID && FAA=${ID}.faa.gz && zcat ${FAA} | muscle -out ${ID}.msa
    done

Preferably without an intermediate script


alignment


bash


parallel

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