Commit 8dde433c authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
Browse files

add rulegraph - add spike-in in bamcoverage - add do to dedup

parent b4fe9787
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......@@ -271,20 +271,23 @@ differential_analysis:
input_counting: no
#############################################################################
# bamCoverage from Deeptools
# see https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
#
# :Parameters:
#
# - do: if 'no', this rule is ignored.
# - options: any parameter recognized by Deeptools (see Deeptools manual)
#
#===============================================================================
# - do: if unchecked, this rule is ignored
# - options: options related to deeptools
# - spike-in: set to yes to use spike-in data as sacaling factor
# see https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
# for more information about effective Genome Size
bamCoverage:
do: yes
options: "--binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC"
spike-in: yes
threads: 4
#############################################################################
......
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......@@ -32,12 +32,20 @@ rule bamCoverage:
singularity:
"epeak.img"
params:
options = bamCoverage_options
options = bamCoverage_options,
scaleFactor = bamCoverage_scaleFactor
envmodules:
"deepTools"
threads:
config['bamCoverage']['threads']
shell:
"""
bamCoverage --bam {input} --outFileName {output} {params.options} --numberOfProcessors {threads} 2> {log.out}
if [[ -s {params.scaleFactor} && {params.scaleFactor} == *"_scaleFactor.txt"* ]]
then
S=$(cat {params.scaleFactor})
bamCoverage --bam {input} --outFileName {output} {params.options} --scaleFactor $S --numberOfProcessors {threads} 2> {log.out}
else
bamCoverage --bam {input} --outFileName {output} {params.options} --numberOfProcessors {threads} 2> {log.out}
fi
"""
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