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Fix error messages #248

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Merged
merged 3 commits into from
Mar 28, 2023
Merged

Fix error messages #248

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cab24bd
Update workflow files
jasmezz Mar 27, 2023
d524831
Update changelog
jasmezz Mar 27, 2023
063db6f
Need some commit to re-start GHA
jasmezz Mar 27, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#237](https://github.com/nf-core/funcscan/pull/237) Reactivate DeepARG automatic database downloading and CI tests as server is now back up. (by @jfy133)
- [#235](https://github.com/nf-core/funcscan/pull/235) Improved annotation speed by switching off pipeline-irrelevant Bakta annotation steps by default. (by @jasmezz)
- [#235](https://github.com/nf-core/funcscan/pull/235) Renamed parameter `annotation_bakta_db` to `annotation_bakta_db_localpath`. (by @jasmezz)
- [#248](https://github.com/nf-core/funcscan/pull/248) Applied best-practice `error("message")` to all (sub)workflow files. (by @jasmezz)

### `Dependencies`

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4 changes: 2 additions & 2 deletions subworkflows/local/amp.nf
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Expand Up @@ -55,7 +55,7 @@ workflow AMP {

// HMMSEARCH
if ( !params.amp_skip_hmmsearch ) {
if ( params.amp_hmmsearch_models ) { ch_amp_hmm_models = Channel.fromPath( params.amp_hmmsearch_models, checkIfExists: true ) } else { exit 1, '[nf-core/funcscan] error: hmm model files not found for --amp_hmmsearch_models! Please check input.' }
if ( params.amp_hmmsearch_models ) { ch_amp_hmm_models = Channel.fromPath( params.amp_hmmsearch_models, checkIfExists: true ) } else { error('[nf-core/funcscan] error: hmm model files not found for --amp_hmmsearch_models! Please check input.') }

ch_amp_hmm_models_meta = ch_amp_hmm_models
.map {
Expand Down Expand Up @@ -104,7 +104,7 @@ workflow AMP {
.multiMap{
input: [ it[0] ]
summary: it[1]
}
}

ch_tabix_input = Channel.of(['id':'ampcombi_complete_summary'])
.combine(ch_ampcombi_summaries_out.summary.collectFile(name: 'ampcombi_complete_summary.csv', keepHeader:true))
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2 changes: 1 addition & 1 deletion subworkflows/local/bgc.nf
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Expand Up @@ -156,7 +156,7 @@ workflow BGC {

// HMMSEARCH
if ( !params.bgc_skip_hmmsearch ) {
if ( params.bgc_hmmsearch_models ) { ch_bgc_hmm_models = Channel.fromPath( params.bgc_hmmsearch_models, checkIfExists: true ) } else { exit 1, '[nf-core/funcscan] error: hmm model files not found for --bgc_hmmsearch_models! Please check input.' }
if ( params.bgc_hmmsearch_models ) { ch_bgc_hmm_models = Channel.fromPath( params.bgc_hmmsearch_models, checkIfExists: true ) } else { error('[nf-core/funcscan] error: hmm model files not found for --bgc_hmmsearch_models! Please check input.') }

ch_bgc_hmm_models_meta = ch_bgc_hmm_models
.map {
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2 changes: 1 addition & 1 deletion subworkflows/local/input_check.nf
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Expand Up @@ -27,7 +27,7 @@ def create_input_channels(LinkedHashMap row) {

def array = []
if (!file(row.fasta).exists()) {
exit 1, "[funscan] error: please check input samplesheet. FASTA file does not exist for: \n${row.fasta}"
error("[funscan] error: please check input samplesheet. FASTA file does not exist for: \n${row.fasta}")
} else {
array = [ meta, file(row.fasta) ]
}
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8 changes: 4 additions & 4 deletions workflows/funcscan.nf
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Expand Up @@ -18,7 +18,7 @@ def checkPathParamList = [ params.input, params.multiqc_config, params.annotatio
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }

// Check mandatory parameters
if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
if (params.input) { ch_input = file(params.input) } else { error("Input samplesheet not specified!") }

// Validate fARGene inputs
// Split input into array, find the union with our valid classes, extract only
Expand All @@ -34,17 +34,17 @@ def fargene_user_classes = fargene_classes.tokenize(',')
def fargene_classes_valid = fargene_user_classes.intersect( fargene_valid_classes )
def fargene_classes_missing = fargene_user_classes - fargene_classes_valid

if ( fargene_classes_missing.size() > 0 ) exit 1, "[nf-core/funcscan] ERROR: invalid class present in --arg_fargene_hmmodel. Please check input. Invalid class: ${fargene_classes_missing.join(', ')}"
if ( fargene_classes_missing.size() > 0 ) error("[nf-core/funcscan] ERROR: invalid class present in --arg_fargene_hmmodel. Please check input. Invalid class: ${fargene_classes_missing.join(', ')}")

// Validate antiSMASH inputs
// 1. Make sure that either both or none of the antiSMASH directories are supplied
if ( ( params.run_bgc_screening && !params.bgc_antismash_databases && params.bgc_antismash_installationdirectory && !params.bgc_skip_antismash) || ( params.run_bgc_screening && params.bgc_antismash_databases && !params.bgc_antismash_installationdirectory && !params.bgc_skip_antismash ) ) exit 1, "[nf-core/funcscan] ERROR: You supplied either the antiSMASH database or its installation directory, but not both. Please either supply both directories or none (letting the pipeline download them instead)."
if ( ( params.run_bgc_screening && !params.bgc_antismash_databases && params.bgc_antismash_installationdirectory && !params.bgc_skip_antismash) || ( params.run_bgc_screening && params.bgc_antismash_databases && !params.bgc_antismash_installationdirectory && !params.bgc_skip_antismash ) ) error("[nf-core/funcscan] ERROR: You supplied either the antiSMASH database or its installation directory, but not both. Please either supply both directories or none (letting the pipeline download them instead).")

// 2. If both are supplied: Exit if we have a name collision error
else if ( params.run_bgc_screening && params.bgc_antismash_databases && params.bgc_antismash_installationdirectory && !params.bgc_skip_antismash ) {
antismash_database_dir = new File(params.bgc_antismash_databases)
antismash_install_dir = new File(params.bgc_antismash_installationdirectory)
if ( antismash_database_dir.name == antismash_install_dir.name ) exit 1, "[nf-core/funcscan] ERROR: Your supplied antiSMASH database and installation directories have identical names: \"" + antismash_install_dir.name + "\".\nPlease make sure to name them differently, for example:\n - Database directory: "+ antismash_database_dir.parent + "/antismash_db\n - Installation directory: " + antismash_install_dir.parent + "/antismash_dir"
if ( antismash_database_dir.name == antismash_install_dir.name ) error("[nf-core/funcscan] ERROR: Your supplied antiSMASH database and installation directories have identical names: \"" + antismash_install_dir.name + "\".\nPlease make sure to name them differently, for example:\n - Database directory: "+ antismash_database_dir.parent + "/antismash_db\n - Installation directory: " + antismash_install_dir.parent + "/antismash_dir")
}

// 3. Give warning if not using container system assuming conda
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