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Change chromap arguments and more fixes #290
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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
ofchromap
includes the--remove-pcr-duplicates
argument and hence, the bam files yielded by the alignment process do not contain duplicates and make thePRESEQ_LCEXTRAP
fails and also prevent obtaining the stats produced bypicard
during the removal of the duplicates. For this reason, thechromap
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 thetest
profile , the reason is summarized in Test for chromap failing #291. Since the problem is that thebam
files for paired-end data produced bychromap
can not be used bymacs2
, 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 fromDESEQ2_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 updatedCHANGELOG.md
is updatedREADME.md
is updatedCloses #288