Add no_fail option to integrity for nextflow to not die

[MatBarba]

Add a --no_fail argument to the check_integrity.py script. The default behaviour is still to fail when an integrity fails (most notably for the genome loader).

This PR changes the default manifest integrity Nextflow module to use that --no_fail option so as to not kill the whole pipeline when an integrity check fails. Instead, integrity.out files are created in each folder and only kept if there have been errors. .

Impacted pipelines: prepare_genome, additional_seq_prepare, dump_files

PS: We should think about writing a final report (sent by email or printed to screen/file) to show what went wrong at the end of a pipeline.

[JAlvarezJarreta]

Regarding the final report, I believe @Dishalodha was looking into something on those lines a couple of months back.

[vsitnik]

Cool. Thank you!