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Code Issues Releases Packages Activity

NOW commit the adapte rtrim flag

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This commit is contained in:
James Fellows Yates 2022-03-30 11:31:37 +02:00
parent 98a9688329
commit 76e9624e3f
3 changed files with 3 additions and 3 deletions
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2
conf/modules.config
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@ -68,7 +68,7 @@ process {
// collapsing options - option to retain singletons // collapsing options - option to retain singletons
params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged", params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
// trimming options // trimming options
params.shortread_clipmerge_skiptrim ? "--disable_adapter_trimming" : "", params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "", params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
!{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : "", !{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : "",
// filtering options // filtering options

2
nextflow.config
View file

@ -57,7 +57,7 @@ params {
// FASTQ preprocessing // FASTQ preprocessing
shortread_clipmerge = false shortread_clipmerge = false
shortread_clipmerge_tool = 'fastp' shortread_clipmerge_tool = 'fastp'
shortread_clipmerge_skiptrim = false shortread_clipmerge_skipadaptertrim = false
shortread_clipmerge_mergepairs = false shortread_clipmerge_mergepairs = false
shortread_clipmerge_excludeunmerged = true shortread_clipmerge_excludeunmerged = true
shortread_clipmerge_adapter1 = null shortread_clipmerge_adapter1 = null

2
nextflow_schema.json
View file

@ -286,7 +286,7 @@
"type": "string", "type": "string",
"default": "fastp" "default": "fastp"
}, },
"shortread_clipmerge_skiptrim": { "shortread_clipmerge_skipadaptertrim": {
"type": "boolean" "type": "boolean"
}, },
"shortread_clipmerge_mergepairs": { "shortread_clipmerge_mergepairs": {