8000 SL-117 fix featurecounts spec · Pull Request #27 · nf-core/rnasplice · GitHub
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SL-117 fix featurecounts spec #27

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Merged
1 commit merged into from
Nov 3, 2022
Merged

SL-117 fix featurecounts spec #27

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2 changes: 1 addition & 1 deletion conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -439,7 +439,7 @@ if (params.edger_exon) {
ext.args = [
'-F GTF',
"-t exon",
params.gencode ? "-g gene_type" : "-g ${params.featurecounts_group_type}",
"-g ${params.gtf_group_features}",
'-f',
'-O',
'-B',
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4 changes: 1 addition & 3 deletions nextflow.config
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Expand Up @@ -22,8 +22,6 @@ params {
gtf_extra_attributes = 'gene_name'
gtf_group_features = 'gene_id'
gencode = false
featurecounts_group_type = 'gene_biotype'
featurecounts_feature_type = 'exon'
save_reference = false

// Trimming
Expand Down Expand Up @@ -306,4 +304,4 @@ def check_max(obj, type) {
return obj
}
}
}
}
1 change: 0 additions & 1 deletion subworkflows/local/prepare_genome.nf
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Expand Up @@ -30,7 +30,6 @@ workflow PREPARE_GENOME {
take:

prepare_tool_indices // list : tools to prepare indices for
biotype // string : if additional fasta file is provided biotype value to use when appending entries to GTF file
is_aws_igenome // boolean: whether the genome files are from AWS iGenomes

main:
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3 changes: 0 additions & 3 deletions workflows/rnasplice.nf
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Expand Up @@ -121,11 +121,8 @@ workflow RNASPLICE {
// SUBWORKFLOW: Uncompress and prepare reference genome files
//

def biotype = params.gencode ? "gene_type" : params.featurecounts_group_type

PREPARE_GENOME (
prepareToolIndices,
biotype,
is_aws_igenome
)

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0