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Update workflows/taxprofiler.nf

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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
This commit is contained in:
Rafal Stepien 2022-09-19 09:51:25 -04:00 committed by Rafal Stepien
parent 0ccbf50938
commit 1584d6fc51
3 changed files with 10 additions and 22 deletions
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4
nextflow_schema.json
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@ -10,13 +10,13 @@
"type": "object", "type": "object",
"fa_icon": "fas fa-terminal", "fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.", "description": "Define where the pipeline should find input data and save output data.",
"required": [ "input", "outdir", "databases"], "required": ["input", "outdir", "databases"],
"properties": { "properties": {
"input": { "input": {
"type": "string", "type": "string",
"format": "file-path", "format": "file-path",
"mimetype": "text/csv", "mimetype": "text/csv",
"pattern": "^\\S+\\.(csv|yaml)$", "pattern": "^\\S+\\.(csv|yaml|yml)$",
"schema": "assets/schema_input.json", "schema": "assets/schema_input.json",
"description": "Path to comma-separated file containing information about the samples and libraries/runs.", "description": "Path to comma-separated file containing information about the samples and libraries/runs.",
"help_text": "You will need to create a design file with information about the samples and libraries/runs you want to running in your pipeline run. Use this parameter to specify its location. It has to be a comma-separated file with 6 columns, and a header row. See [usage docs](https://nf-co.re/taxprofiler/usage#samplesheet-input).", "help_text": "You will need to create a design file with information about the samples and libraries/runs you want to running in your pipeline run. Use this parameter to specify its location. It has to be a comma-separated file with 6 columns, and a header row. See [usage docs](https://nf-co.re/taxprofiler/usage#samplesheet-input).",

6
subworkflows/local/input_check.nf
View file

@ -9,11 +9,11 @@ include { EIDO_CONVERT } from '../../modules/nf-core/modules/eido/convert/main'
workflow INPUT_CHECK { workflow INPUT_CHECK {
take: take:
samplesheet_or_pep_config // file: /path/to/samplesheet.csv or /path/to/pep/config.yaml samplesheet_or_pep_config // file: /path/to/samplesheet.csv or /path/to/pep/config.yaml
ch_pep_input_base_dir pep_input_base_dir
main: main:
EIDO_VALIDATE ( samplesheet_or_pep_config, file("$projectDir/assets/samplesheet_schema.yaml"), ch_pep_input_base_dir ) EIDO_VALIDATE ( samplesheet_or_pep_config, file("$projectDir/assets/samplesheet_schema.yaml"), pep_input_base_dir )
converted_samplesheet = EIDO_CONVERT ( samplesheet_or_pep_config, "csv", ch_pep_input_base_dir ) converted_samplesheet = EIDO_CONVERT ( samplesheet_or_pep_config, "csv", pep_input_base_dir )
parsed_samplesheet = SAMPLESHEET_CHECK ( converted_samplesheet.samplesheet_converted ) parsed_samplesheet = SAMPLESHEET_CHECK ( converted_samplesheet.samplesheet_converted )
.csv .csv
.splitCsv ( header:true, sep:',' ) .splitCsv ( header:true, sep:',' )

22
workflows/taxprofiler.nf
View file

@ -17,23 +17,11 @@ def checkPathParamList = [ params.input, params.databases, params.hostremoval_re
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
// Check mandatory parameters // Check mandatory parameters
if ( params.input.endsWith(".yaml") ) { if ( params.input ) {
ch_input = file(params.input, checkIfExists: true)
if ( params.input.startsWith("http://") || params.input.startsWith("https://") ) { pep_input_base_dir = file(params.input).extension.matches("yaml|yml") ? file(file(params.input).getParent(), checkIfExists: true) : []
ch_input = file(params.input)
ch_pep_input_base_dir = []
}
else {
ch_input = file(params.input)
ch_pep_input_base_dir = new File(params.input).getParent()
}
} else if ( params.input.endsWith(".csv") ) {
ch_input = file(params.input)
ch_pep_input_base_dir = []
} else { } else {
exit 1, 'Input samplesheet or PEP config not specified!' exit 1, "Input samplesheet, or PEP config and base directory not specified"
} }
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' } if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
@ -116,7 +104,7 @@ workflow TAXPROFILER {
SUBWORKFLOW: Read in samplesheet, validate and stage input files SUBWORKFLOW: Read in samplesheet, validate and stage input files
*/ */
INPUT_CHECK ( INPUT_CHECK (
ch_input, ch_pep_input_base_dir ch_input, pep_input_base_dir
) )
ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)