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https://github.com/MillironX/taxprofiler.git
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Merge pull request #280 from nf-core/replace-exit-with-error
Replace all instance of exit 1 with error for safety and consistency
This commit is contained in:
commit
c3c91780ab
4 changed files with 21 additions and 20 deletions
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@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [#269](https://github.com/nf-core/taxprofiler/pull/269/files) Reduced output files in AWS full test output due to very large files
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- [#270](https://github.com/nf-core/taxprofiler/pull/270/files) Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133)
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- [#274](https://github.com/nf-core/taxprofiler/pull/274/files) Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam)
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- [#275](https://github.com/nf-core/taxprofiler/pull/275/files) Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133)
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### `Dependencies`
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@ -22,7 +22,7 @@ workflow DB_CHECK {
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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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if ( unique_names.size() < db_name.size() ) error("[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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@ -55,24 +55,24 @@ workflow DB_CHECK {
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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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if (row.size() < 4) error("[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_headers.join(", ")}"
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if ( !row.keySet().containsAll(expected_headers) ) error("[nf-core/taxprofiler] ERROR: Invalid database input sheet - malformed column names. Please check input TSV. Column names should be: ${expected_headers.join(", ")}")
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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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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) ) error("[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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if ( row.db_params.contains('"') ) error("[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}")
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if ( row.db_params.contains("'") ) error("[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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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(";") ) error("[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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if (!file(row.db_path, type: 'dir').exists()) error("ERROR: Please check input samplesheet -> database path could not be found!\n${row.db_path}")
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}
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@ -44,7 +44,7 @@ def create_fastq_channel(LinkedHashMap row) {
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// add path(s) of the fastq file(s) to the meta map
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if (!file(row.fastq_1).exists()) {
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exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
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error("ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}")
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}
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if (meta.single_end) {
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@ -52,12 +52,12 @@ def create_fastq_channel(LinkedHashMap row) {
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} else {
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if (meta.instrument_platform == 'OXFORD_NANOPORE') {
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if (row.fastq_2 != '') {
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exit 1, "ERROR: Please check input samplesheet -> For Oxford Nanopore reads Read 2 FastQ should be empty!\n${row.fastq_2}"
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error("ERROR: Please check input samplesheet -> For Oxford Nanopore reads Read 2 FastQ should be empty!\n${row.fastq_2}")
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}
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return [ meta, [ file(row.fastq_1) ] ]
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} else {
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if (!file(row.fastq_2).exists()) {
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exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
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error("ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}")
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}
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return [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
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}
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@ -72,7 +72,7 @@ def create_fasta_channel(LinkedHashMap row) {
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meta.is_fasta = true
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if (!file(row.fasta).exists()) {
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exit 1, "ERROR: Please check input samplesheet -> FastA file does not exist!\n${row.fasta}"
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error("ERROR: Please check input samplesheet -> FastA file does not exist!\n${row.fasta}")
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}
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return [ meta, [ file(row.fasta) ] ]
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}
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@ -24,19 +24,19 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
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if ( params.input ) {
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ch_input = file(params.input, checkIfExists: true)
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} else {
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exit 1, "Input samplesheet not specified"
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error("Input samplesheet not specified")
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}
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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.databases) { ch_databases = file(params.databases, checkIfExists: true) } else { error('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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if (params.shortread_qc_includeunmerged && !params.shortread_qc_mergepairs) error("ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging is not turned on. Please specify --shortread_qc_mergepairs")
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if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_qc == false || params.shortread_qc_tool != 'fastp' )) exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_qc and/or --shortread_qc_tool 'fastp'"
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if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_qc == false || params.shortread_qc_tool != 'fastp' )) error("ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_qc and/or --shortread_qc_tool 'fastp'")
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if (params.perform_shortread_hostremoval && !params.hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --hostremoval_reference FASTA supplied. Check input." }
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if (params.perform_shortread_hostremoval && !params.hostremoval_reference && params.shortread_hostremoval_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input." }
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if (params.perform_longread_hostremoval && !params.hostremoval_reference && params.longread_hostremoval_index) { exit 1, "ERROR: [nf-core/taxprofiler] --longread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input." }
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if (params.perform_shortread_hostremoval && !params.hostremoval_reference) { error("ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --hostremoval_reference FASTA supplied. Check input.") }
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if (params.perform_shortread_hostremoval && !params.hostremoval_reference && params.shortread_hostremoval_index) { error("ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input.") }
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if (params.perform_longread_hostremoval && !params.hostremoval_reference && params.longread_hostremoval_index) { error("ERROR: [nf-core/taxprofiler] --longread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input.") }
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if (params.hostremoval_reference ) { ch_reference = file(params.hostremoval_reference) }
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if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = Channel.fromPath(params.shortread_hostremoval_index).map{[[], it]} } else { ch_shortread_reference_index = [] }
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@ -45,7 +45,7 @@ if (params.longread_hostremoval_index ) { ch_longread_reference_index = fi
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if (params.diamond_save_reads ) log.warn "[nf-core/taxprofiler] DIAMOND only allows output of a single format. As --diamond_save_reads supplied, only aligned reads in SAM format will be produced, no taxonomic profiles will be available."
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if (params.run_malt && params.run_krona && !params.krona_taxonomy_directory) log.warn "[nf-core/taxprofiler] Krona can only be run on MALT output if path to Krona taxonomy database supplied to --krona_taxonomy_directory. Krona will not be executed in this run for MALT."
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if (params.run_bracken && !params.run_kraken2) exit 1, 'ERROR: [nf-core/taxprofiler] You are attempting to run Bracken without running kraken2. This is not possible! Please set --run_kraken2 as well.'
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if (params.run_bracken && !params.run_kraken2) error('ERROR: [nf-core/taxprofiler] You are attempting to run Bracken without running kraken2. This is not possible! Please set --run_kraken2 as well.')
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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