mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 23:13:09 +00:00
76 lines
2.6 KiB
Text
76 lines
2.6 KiB
Text
//
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// Check input samplesheet and get read channels
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//
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include { UNTAR } from '../../modules/nf-core/untar/main'
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workflow DB_CHECK {
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take:
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dbsheet // file: /path/to/dbsheet.csv
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main:
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ch_versions = Channel.empty()
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// TODO: make database sheet check
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// Checks:
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// 1) no duplicates,
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parsed_samplesheet = Channel.fromPath(dbsheet)
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.splitCsv ( header:true, sep:',' )
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.map {
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validate_db_sheet(it)
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create_db_channels(it)
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}
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ch_dbs_for_untar = parsed_samplesheet
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.branch {
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untar: it[1].toString().endsWith(".tar.gz")
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skip: true
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}
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// TODO Filter to only run UNTAR on DBs of tools actually using?
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// TODO make optional whether to save
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UNTAR ( ch_dbs_for_untar.untar )
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ch_versions = ch_versions.mix(UNTAR.out.versions.first())
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ch_final_dbs = ch_dbs_for_untar.skip.mix( UNTAR.out.untar )
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emit:
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dbs = ch_final_dbs // channel: [ val(meta), [ db ] ]
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versions = ch_versions // channel: [ versions.yml ]
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}
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def validate_db_sheet(LinkedHashMap row){
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// check minimum number of columns
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if (row.size() < 4) exit 1, "[nf-core/taxprofiler] error: Invalid database input sheet - malformed row (e.g. missing column). See documentation for more information. Error in: ${row}, "
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// all columns there
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def expected_headers = ['tool', 'db_name', 'db_params', 'db_path']
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if ( !row.keySet().containsAll(expected_headers) ) exit 1, "[nf-core/taxprofiler] error: Invalid database input sheet - malformed column names. Please check input TSV. Column names should be: ${expected_keys.join(", ")}"
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// valid tools specified// TIFNISIH LIST
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def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "malt", "metaphlan3" ]
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// detect quotes in params
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if ( row.db_params.contains('"') ) exit 1, "[nf-core/taxprofiler] error: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
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if ( row.db_params.contains("'") ) exit 1, "[nf-core/taxprofiler] error: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
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}
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def create_db_channels(LinkedHashMap row) {
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def meta = [:]
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meta.tool = row.tool
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meta.db_name = row.db_name
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meta.db_params = row.db_params
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def array = []
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if (!file(row.db_path, type: 'dir').exists()) {
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exit 1, "ERROR: Please check input samplesheet -> database could not be found!\n${row.db_path}"
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}
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array = [ meta, file(row.db_path) ]
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return array
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}
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