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partly fixes #116 - params for featurecounts #118

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merged 6 commits into from
Dec 14, 2020

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MarieLataretu
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  • added additional params for featurecounts

@@ -487,7 +487,7 @@ workflow expression_reference_based {

main:
// count with featurecounts
featurecounts(sample_bam_ch, annotation)
featurecounts(sample_bam_ch, annotation, params.featurecounts_additional_params)
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why @MarieLataretu ? You can directly access params.featurecounts_additional_params from within the process (params are global) and you don't have to pass the parameter. Or do you want to be more explicit?

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I think, this makes it clearer that the process depends on this parameter!

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agree!

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nextflow.config Outdated
@@ -29,7 +29,8 @@ params {
mode = 'single'
tpm = 1
fastp_additional_params = '-5 -3 -W 4 -M 20 -l 15 -x -n 5 -z 6'
histat2_additional_params = ''
hisat2_additional_params = ''
featurecounts_additional_params = ''
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do we want to put the default parameters here? Because then they would also occur in the help and give a better idea of how to use this parameter. Suggestion:

featurecounts_additional_params = '-t gene -g gene_id'

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I like that!

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generally approve! I corrected few typos (histat --> hisat, ...)

And see my suggestions

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@MarieLataretu MarieLataretu merged commit 4f2644d into master Dec 14, 2020
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2 participants