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NOW commit the adapte rtrim flag
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parent
98a9688329
commit
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3 changed files with 3 additions and 3 deletions
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@ -68,7 +68,7 @@ process {
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// collapsing options - option to retain singletons
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params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
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// trimming options
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params.shortread_clipmerge_skiptrim ? "--disable_adapter_trimming" : "",
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params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
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params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
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!{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : "",
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// filtering options
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@ -57,7 +57,7 @@ params {
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// FASTQ preprocessing
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shortread_clipmerge = false
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shortread_clipmerge_tool = 'fastp'
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shortread_clipmerge_skiptrim = false
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shortread_clipmerge_skipadaptertrim = false
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shortread_clipmerge_mergepairs = false
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shortread_clipmerge_excludeunmerged = true
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shortread_clipmerge_adapter1 = null
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@ -286,7 +286,7 @@
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"type": "string",
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"default": "fastp"
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},
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"shortread_clipmerge_skiptrim": {
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"shortread_clipmerge_skipadaptertrim": {
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"type": "boolean"
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},
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"shortread_clipmerge_mergepairs": {
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