Some more AWS issues

[apeltzer]

107[a3/57447f] Submitted process > endorSpy (JK2782)
108WARN: Directive 'validExitStatus' has been deprecated -- Check process 'nuclear_contamination'
109[94/330326] Submitted process > preseq (JK2782)
110Error executing process > 'sex_deterrmine'
111Caused by:
112  Can't stage file file:///NO_FILE -- file does not exist
113Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

[jfy133]

Should follow more the examples of e.g .viralrecon:

https://github.com/nf-core/viralrecon/blob/69326f97b1c1d1b8733a0df573cb1f3eff907e6d/main.nf#L163

and ch_fasta = file(params.fasta)

And then use proper

input:
    path fasta from ch_fasta

From the original issue report #472

[jfy133]

Had a successful run the other day. Running few last checks