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refactor: simplify DB validation
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parent
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commit
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1 changed files with 20 additions and 34 deletions
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@ -28,9 +28,9 @@ workflow DB_CHECK {
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// Normal checks for within-row validity, so can be moved to separate functions
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// Normal checks for within-row validity, so can be moved to separate functions
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parsed_samplesheet = Channel.fromPath(dbsheet)
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parsed_samplesheet = Channel.fromPath(dbsheet)
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.splitCsv ( header:true, sep:',' )
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.splitCsv ( header:true, sep:',' )
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.map {
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.map { row ->
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validate_db_rows(it)
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validate_db_rows(row)
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create_db_channels(it)
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return [ row.subMap(['tool', 'db_name', 'db_params']), file(row.db_path) ]
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}
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}
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ch_dbs_for_untar = parsed_samplesheet
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ch_dbs_for_untar = parsed_samplesheet
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@ -54,41 +54,27 @@ workflow DB_CHECK {
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versions = ch_versions // channel: [ versions.yml ]
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versions = ch_versions // channel: [ versions.yml ]
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}
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}
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def validate_db_rows(LinkedHashMap row){
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def validate_db_rows(LinkedHashMap row) {
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// check minimum number of columns
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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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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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// all columns there
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def expected_headers = ['tool', 'db_name', 'db_params', 'db_path']
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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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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
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// valid tools specified
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def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
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def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
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if ( !expected_tools.contains(row.tool) ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid tool name. Please see documentation for all supported profilers. Error in: ${row}"
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if ( !expected_tools.contains(row.tool) ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid tool name. Please see documentation for all supported profilers. Error in: ${row}"
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// detect quotes in params
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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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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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// check if any form of bracken params, that it must have `;`
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// check if any form of bracken params, that it must have `;`
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if ( row.tool == 'bracken' && row.db_params && !row.db_params.contains(";") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. Bracken requires a semi-colon if passing parameter. Error in: ${row}"
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if ( row.tool == 'bracken' && row.db_params && !row.db_params.contains(";") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. Bracken requires a semi-colon if passing parameter. Error in: ${row}"
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// ensure that the database directory exists
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if (!file(row.db_path, type: 'dir').exists()) exit 1, "ERROR: Please check input samplesheet -> database path could not be found!\n${row.db_path}"
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}
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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 path 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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