Merge pull request #248 from nf-core/fix-error-messages

Fix error messages

Author: jasmezz

CHANGELOG.md

@@ -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`
 

subworkflows/local/amp.nf

@@ -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 {
@@ -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))

subworkflows/local/bgc.nf

@@ -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 {

subworkflows/local/input_check.nf

@@ -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) ]
     }

workflows/funcscan.nf

@@ -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
@@ -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