Adjusted fixes for AWS index handling

[apeltzer]

Our handling of indices wasn't properly done I fear, so this is an attempt to get that fixed :-)

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker --paired_end).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

[jfy133]

@apeltzer and I got the benchmarking_vikingfish profile to work on AWS 🎉 !

However the remaining tests don't work properly (see my notes)

## TO CHECK! No mapping?
nextflow run ../../main.nf -profile test_tsv,docker --skip_collapse
## TO CHECK - one sample?
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_pretrim,docker --skip_trim
## TO CHECK - no mapping?
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --skip_adapterremoval
## TO CHECK - no mapping?
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --skip_adapterremoval --run_convertinputbam

[jfy133]

LGTM now. This includes a lot of minor fixes as well as AWS. But should be good once our final AWS pass goes (dreamy_venter). Then MERGE @apelter (finally!).

Up to you if you want to run the small test profiles too on AWS first...

[jfy133]

Suggested change

	If you want to use pre-existing `bwa index` indices, please supply the **directory** to the FASTA you also specified in `--fasta` (see above). EAGER2 will automagically detect the index files by searching for the FASTA filename with the corresponding `bwa` index file suffixes.
	If you want to use pre-existing `bwa index` indices, please supply the **directory** to the FASTA you also specified in `--fasta` (see above). nf-core/eager will automagically detect the index files by searching for the FASTA filename with the corresponding `bwa` index file suffixes.