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https://github.com/MillironX/taxprofiler.git
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Merge pull request #189 from nf-core/database-check
Adds (native groovy!) database check
This commit is contained in:
commit
578081df2e
5 changed files with 49 additions and 53 deletions
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@ -12,14 +12,6 @@
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process {
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withName: DATABASE_CHECK {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: FASTQC {
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ext.args = '--quiet'
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ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
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@ -1,29 +0,0 @@
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process DATABASE_CHECK {
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tag "$databasesheet"
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label 'process_single'
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conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/python:3.8.3' :
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'quay.io/biocontainers/python:3.8.3' }"
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input:
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path databasesheet
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output:
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path '*.csv' , emit: csv
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script: // This script is bundled with the pipeline, in nf-core/taxprofiler/bin/
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"""
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cat $databasesheet >> database_sheet.valid.csv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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python: \$(python --version | sed 's/Python //g')
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END_VERSIONS
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"""
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}
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@ -2,7 +2,6 @@
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// Check input samplesheet and get read channels
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//
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include { DATABASE_CHECK } from '../../modules/local/database_check'
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include { UNTAR } from '../../modules/nf-core/untar/main'
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workflow DB_CHECK {
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@ -10,15 +9,27 @@ workflow DB_CHECK {
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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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// 2) args do not have quotes, e.g. just `,,` and NOT `,"",`
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parsed_samplesheet = DATABASE_CHECK ( dbsheet )
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.csv
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// special check to check _between_ rows, for which we must group rows together
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// note: this will run in parallel to within-row validity, but we can assume this will run faster thus will fail first
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Channel.fromPath(dbsheet)
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.splitCsv ( header:true, sep:',' )
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.map {[it.tool, it.db_name] }
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.groupTuple()
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.map {
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tool, db_name ->
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def unique_names = db_name.unique(false)
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if ( unique_names.size() < db_name.size() ) exit 1, "[nf-core/taxprofiler] ERROR: Each database for a tool must have a unique name, duplicated detected. Tool: ${tool}, Database name: ${unique_names}"
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}
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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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.splitCsv ( header:true, sep:',' )
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.map { create_db_channels(it) }
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.map {
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validate_db_rows(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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@ -29,12 +40,32 @@ workflow DB_CHECK {
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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 = DATABASE_CHECK.out.versions.mix(UNTAR.out.versions.first()) // channel: [ versions.yml ]
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versions = ch_versions // channel: [ versions.yml ]
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}
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def validate_db_rows(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", "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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// 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: ${row}"
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}
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def create_db_channels(LinkedHashMap row) {
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@ -45,9 +76,11 @@ def create_db_channels(LinkedHashMap row) {
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def array = []
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if (!file(row.db_path, type: 'dir').exists()) {
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exit 1, "ERROR: Please check input samplesheet -> database could not be found!\n${row.db_path}"
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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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@ -41,14 +41,14 @@ workflow PROFILING {
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}
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.combine(databases)
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.branch {
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malt: it[2]['tool'] == 'malt'
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kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken' // to reuse the kraken module to produce the input data for bracken
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metaphlan3: it[2]['tool'] == 'metaphlan3'
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centrifuge: it[2]['tool'] == 'centrifuge'
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kaiju: it[2]['tool'] == 'kaiju'
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diamond: it[2]['tool'] == 'diamond'
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motus: it[2]['tool'] == 'motus'
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kaiju: it[2]['tool'] == 'kaiju'
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kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken' // to reuse the kraken module to produce the input data for bracken
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krakenuniq: it[2]['tool'] == 'krakenuniq'
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malt: it[2]['tool'] == 'malt'
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metaphlan3: it[2]['tool'] == 'metaphlan3'
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motus: it[2]['tool'] == 'motus'
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unknown: true
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}
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@ -25,7 +25,7 @@ if ( params.input ) {
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exit 1, "Input samplesheet, or PEP config and base directory not specified"
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}
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if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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if (params.databases) { ch_databases = file(params.databases, checkIfExists: true) } else { exit 1, 'Input database sheet not specified!' }
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if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
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if (params.shortread_qc_includeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging is not turned on. Please specify --shortread_qc_mergepairs"
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