mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-21 21:06:03 +00:00
refactor: simplify DB validation
This commit is contained in:
parent
53db964bcf
commit
c2ad421051
1 changed files with 20 additions and 34 deletions
|
@ -28,9 +28,9 @@ workflow DB_CHECK {
|
|||
// Normal checks for within-row validity, so can be moved to separate functions
|
||||
parsed_samplesheet = Channel.fromPath(dbsheet)
|
||||
.splitCsv ( header:true, sep:',' )
|
||||
.map {
|
||||
validate_db_rows(it)
|
||||
create_db_channels(it)
|
||||
.map { row ->
|
||||
validate_db_rows(row)
|
||||
return [ row.subMap(['tool', 'db_name', 'db_params']), file(row.db_path) ]
|
||||
}
|
||||
|
||||
ch_dbs_for_untar = parsed_samplesheet
|
||||
|
@ -54,41 +54,27 @@ workflow DB_CHECK {
|
|||
versions = ch_versions // channel: [ versions.yml ]
|
||||
}
|
||||
|
||||
def validate_db_rows(LinkedHashMap row){
|
||||
def validate_db_rows(LinkedHashMap row) {
|
||||
|
||||
// check minimum number of columns
|
||||
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}"
|
||||
// check minimum number of columns
|
||||
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}"
|
||||
|
||||
// all columns there
|
||||
def expected_headers = ['tool', 'db_name', 'db_params', 'db_path']
|
||||
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(", ")}"
|
||||
// all columns there
|
||||
def expected_headers = ['tool', 'db_name', 'db_params', 'db_path']
|
||||
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(", ")}"
|
||||
|
||||
// valid tools specified
|
||||
def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
|
||||
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}"
|
||||
// valid tools specified
|
||||
def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
|
||||
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}"
|
||||
|
||||
// detect quotes in params
|
||||
if ( row.db_params.contains('"') ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
|
||||
if ( row.db_params.contains("'") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
|
||||
// detect quotes in params
|
||||
if ( row.db_params.contains('"') ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
|
||||
if ( row.db_params.contains("'") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
|
||||
|
||||
// check if any form of bracken params, that it must have `;`
|
||||
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}"
|
||||
// check if any form of bracken params, that it must have `;`
|
||||
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: ${row}"
|
||||
|
||||
// ensure that the database directory exists
|
||||
if (!file(row.db_path, type: 'dir').exists()) exit 1, "ERROR: Please check input samplesheet -> database path could not be found!\n${row.db_path}"
|
||||
|
||||
}
|
||||
|
||||
def create_db_channels(LinkedHashMap row) {
|
||||
def meta = [:]
|
||||
meta.tool = row.tool
|
||||
meta.db_name = row.db_name
|
||||
meta.db_params = row.db_params
|
||||
|
||||
def array = []
|
||||
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}"
|
||||
}
|
||||
array = [ meta, file(row.db_path) ]
|
||||
|
||||
return array
|
||||
}
|
||||
|
||||
|
||||
|
|
Loading…
Reference in a new issue