Remapping

[maxulysse]

• Add new remapping step (possibility to remap BAMs)
• fastqFiles renamed to inputFiles
• MapReads for remapping will now convert BAM to FASTQ and feed it to BWA on the fly

PR checklist

• PR is made against dev branch
• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• Ensure the test suite passes (./scripts/test.sh -p docker -t ALL).
• Documentation in docs is updated
• CHANGELOG.md is updated

[maxulysse]

I think we could improve that by checking if input is bam or fastq, and then do the correct thing

[maxulysse]

I'm now happy with my latest changes.
@alneberg @szilvajuhos if you want to comment, approve or not

[maxulysse]

The only thing that is really missing is tests for this new feature...
But as this is an edge case, I'm wondering if we should test it or not.
What do you think?

[alneberg]

We should probably allow fq.gz as well right?

[maxulysse]

We can think of it in the extractSample() function, but currently I can't think of anyone asking me about this particular .fq.gz extension.

[szilvajuhos]

What about the BAM index files in the tsv file example?

[maxulysse]

The index is not in the TSV when mapping BAMs.
I figured that if you want to (re)map BAMs, there's little use of the indexes.

[szilvajuhos]

Looks OK