samtools faidx replaces fasta file with symlink pointing to itself

[samuell]

At least when running samtools-faidx without docker, the input fasta (.fa) file is replaced with a symlink pointing to itself:

[samuel 002-resequencing]$ ll *fa
lrwxrwxrwx 1 samuel samuel 98 maj 18 20:43 Homo_sapiens.GRCh37.75.dna.chromosome.17.fa -> /home/samuel/code/bils/cwl-evaluation/002-resequencing/Homo_sapiens.GRCh37.75.dna.chromosome.17.fa

The problem is solved (at least for me), when uncommenting the .fai part on line 34 in samtools-faidx.cwl, so as to let samtools faidx only return the newly created .fai file.