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Fix mafft alignment for large numbers (~10k) of protein groups.

Henning Schiebenhöfer requested to merge hotfix_mafft_for_many_pgs into master

Fix mafft alignment for large numbers (~10k) of protein groups.

The mafft shell-script failed due to too many arguments/too long lines. This workaround writes the list of files to a text file, which is then read by the run_mafft rule.

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