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partly fixes #116 - params for featurecounts #118
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MarieLataretu
commented
Dec 14, 2020
- added additional params for featurecounts
@@ -487,7 +487,7 @@ workflow expression_reference_based { | |||
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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!
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Outdated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
…ab/rnaflow into MarieLataretu/issue116