Change chromap arguments and more fixes

[JoseEspinosa]

Addressing the following fixes before 2.0.0 release:

• As explained in chromap chipseq default mode remove duplicates making preseq fail #288 the --preset chip of chromap includes the --remove-pcr-duplicates argument and hence, the bam files yielded by the alignment process do not contain duplicates and make the PRESEQ_LCEXTRAP fails and also prevent obtaining the stats produced by picard during the removal of the duplicates. For this reason, the chromap command has been refactored to use all the --preset chip arguments but --remove-pcr-duplicates.
  The CI for chromap has been enable again.

• Chromap failed when running the test profile , the reason is summarized in Test for chromap failing #291. Since the problem is that the bam files for paired-end data produced by chromap can not be used by macs2, these files are now removed from the dataset giving a warning.

• Add back the spreadsheet representation of consensus peak-set across samples with gene annotation columns adding the ANNOTATE_BOOLEAN_PEAKS.

• Emit rds data from DESEQ2_QC process.

• Fix publication of aligners indexes.

• Update usage.md.

• Update output.md.

• 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 (nextflow run . -profile test,docker).

• Make sure your code lints (nf-core lint .).

• Documentation in docs is updated

• CHANGELOG.md is updated

• README.md is updated

Closes #288