diff --git a/conf/modules.config b/conf/modules.config index a9bc3a1..71eaa75 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -68,7 +68,7 @@ process { // collapsing options - option to retain singletons params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged", // 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}" : "", !{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : "", // filtering options diff --git a/nextflow.config b/nextflow.config index a312d0c..6fde513 100644 --- a/nextflow.config +++ b/nextflow.config @@ -57,7 +57,7 @@ params { // FASTQ preprocessing shortread_clipmerge = false shortread_clipmerge_tool = 'fastp' - shortread_clipmerge_skiptrim = false + shortread_clipmerge_skipadaptertrim = false shortread_clipmerge_mergepairs = false shortread_clipmerge_excludeunmerged = true shortread_clipmerge_adapter1 = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 545f990..adc5a73 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -286,7 +286,7 @@ "type": "string", "default": "fastp" }, - "shortread_clipmerge_skiptrim": { + "shortread_clipmerge_skipadaptertrim": { "type": "boolean" }, "shortread_clipmerge_mergepairs": {