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Documentation and how tos for developing eager

How to add new input files and options to the reference sheet

To add new input files or options to the reference sheet, you have to complete all the following steps.

Single-reference input workflow

  1. Add your new parameter to nextflow.config.
  2. Add parameter description to schema (nf-core schema build).
  3. Read in new parameter (params.) as input within the reference_indexing_single local subworkflow.
    1. Add new line to the large .map{} operation starting on line 80 and add check if the file exists. def <PARAM_NAME> = params.<NEW> != null ? file(params.<NEW>, checkIfExists: true ) : ""
    2. Add <PARAM_NAME> to the result of the map operation. Double-check the order!
    3. With the ch_ref_index_single.multiMap{} below you add the reference name as a meta. You can also combine your new parameter with others if useful for the workflow step. <NEW_SUBCHANNE>: [ meta, <PARAM_NAME> ]
    4. Add your ch_ref_index_single.<NEW_SUBCHANNEL> to the final emit. <NEW_EMIT> = ch_ref_index_single.<NEW_SUBCHANNEL>

Multi-reference input workflow

  1. Add new column named <SOFTWARE_FILETYPE> and test data to the test reference sheet (https://github.com/nf-core/test-datasets/blob/eager/reference/reference_sheet_multiref.csv).
  2. Read in new input via nf-validation plugin within the reference_indexing_multi local subworkflow.
    1. Add new "property" <SOFTWARE_FILETYPE> to the fasta validation schema (assets/schema_fasta.json).
      1. Add "type" of your object, e.g. "type": "string" for file paths and "type": "integer" for numbers.
      2. Add "meta": "<NEW_META>" to add your input to the meta map.
      3. Add "format": "file-path" to check if the entered string is a file path.
      4. Add "pattern": "<REGEX_PATTERN>" to check that the string doesn't contain spaces ("pattern": "^\\S+$"), contains a certain file extension ("pattern": "^\\S+\\.vcf$"), etc.
      5. Add "exists": "true" to check if the file exists.
      6. Add an "errorMessage": to be displayed if one of the checks fails describing the criteria above.
    2. Add new line to the large .map{} operation starting on line 22 and add conversion from empty array [] to empty string "". <PARAM_NAME> = <PARAM_NAME> != [] ? <PARAM_NAME> : ""
    3. Add <PARAM_NAME> to the result of the .map{} operation. Double-check the order!
    4. With the ch_input_from_referencesheet.multiMap{} below, you add the reference name as a meta. You can also combine your new parameter with others if useful for the workflow step. <NEW_SUBCHANNEL>: [ meta, <PARAM_NAME> ]
    5. Add ch_input_from_referencesheet.<NEW_SUBCHANNEL> to the final emit. <NEW_EMIT> = ch_input_from_referencesheet.<NEW_SUBCHANNEL>
    6. Add corresponding params.<NEW> to warning on line 23 of the reference indexing subworkflow.

Combining in the Reference Indexing workflow

  1. Add you new parameter channel to the if condition selecting between the direct parameter input or the reference sheet input.
    1. below "REFERENCE_INDEXING_MULTI" for reference sheet input <NEW_CHANNEL> = REFERENCE_INDEXING_MULTI.out.<NEW_EMIT>
    2. below "REFERENCE_INDEXING_SINGLE" <NEW_CHANNEL> = REFERENCE_INDEXING_SINGLE.out.<NEW_EMIT>
    3. Filter out options that have not been provided. <NEW_CHANNEL> = <NEW_CHANNEL>.filter{ it[1] != "" }
    4. Add unzipping of zipped input files with GUNZIP.
    5. Add <NEW_CHANNEL> to the final emit. <NEW_EMIT> = <NEW_CHANNEL>
    6. Call new inputs within the main eager.nf with REFERENCE_INDEXING.out.<NEW_EMIT>.
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