Important! Template update for nf-core/tools v2.8

README.md

@@ -69,10 +69,6 @@ To see the the results of a test run with a full size dataset refer to the [resu
 For more details about the output files and reports, please refer to the
 [output documentation](https://nf-co.re/mag/output).
 
-## Documentation
-
-The nf-core/mag pipeline comes with documentation about the pipeline [usage](https://nf-co.re/mag/usage), [parameters](https://nf-co.re/mag/parameters) and [output](https://nf-co.re/mag/output). Detailed information about how to specify the input can be found under [input specifications](https://nf-co.re/mag/usage#input_specifications).
-
 ### Group-wise co-assembly and co-abundance computation
 
 Each sample has an associated group ID (see [input specifications](https://nf-co.re/mag/usage#input_specifications)). This group information can be used for group-wise co-assembly with `MEGAHIT` or `SPAdes` and/or to compute co-abundances for the binning step with `MetaBAT2`. By default, group-wise co-assembly is disabled, while the computation of group-wise co-abundances is enabled. For more information about how this group information can be used see the documentation for the parameters [`--coassemble_group`](https://nf-co.re/mag/parameters#coassemble_group) and [`--binning_map_mode`](https://nf-co.re/mag/parameters#binning_map_mode).

docs/usage.md

@@ -107,7 +107,7 @@ input: 'data'
 
 You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
 
-See the [nf-core/mag website documentation](https://nf-co.re/mag/usage#usage) for more information about pipeline specific parameters.
+See the [nf-core/mag website documentation](https://nf-co.re/mag/parameters) for more information about pipeline specific parameters.
 
 ### Updating the pipeline
 
@@ -250,8 +250,6 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio
      ```
 
 > **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch.
->
-> > > > > > > origin/dev
 
 ### nf-core/configs
 

lib/NfcoreSchema.groovy

@@ -119,7 +119,7 @@ class NfcoreSchema {
         for (specifiedParam in params.keySet()) {
             // nextflow params
             if (nf_params.contains(specifiedParam)) {
-                log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'"
+                Nextflow.error("ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'")
                 has_error = true
             }
             // unexpected params
@@ -158,7 +158,7 @@ class NfcoreSchema {
             schema.validate(params_json)
         } catch (ValidationException e) {
             println ''
-            log.error 'ERROR: Validation of pipeline parameters failed!'
+            Nextflow.error('ERROR: Validation of pipeline parameters failed!')
             JSONObject exceptionJSON = e.toJSON()
             printExceptions(exceptionJSON, params_json, log, enums)
             println ''
@@ -340,11 +340,11 @@ class NfcoreSchema {
             def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/
             // Missing required param
             if (m.matches()) {
-                log.error "* Missing required parameter: --${m[0][1]}"
+                Nextflow.error("* Missing required parameter: --${m[0][1]}")
             }
             // Other base-level error
             else if (ex_json['pointerToViolation'] == '#') {
-                log.error "* ${ex_json['message']}"
+                Nextflow.error("* ${ex_json['message']}")
             }
             // Error with specific param
             else {
@@ -353,12 +353,12 @@ class NfcoreSchema {
                 if (enums.containsKey(param)) {
                     def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices"
                     if (enums[param].size() > limit) {
-                        log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )"
+                        Nextflow.error("${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )")
                     } else {
-                        log.error "${error_msg}: ${enums[param].join(', ')})"
+                        Nextflow.error("${error_msg}: ${enums[param].join(', ')})")
                     }
                 } else {
-                    log.error "* --${param}: ${ex_json['message']} (${param_val})"
+                    Nextflow.error("* --${param}: ${ex_json['message']} (${param_val})")
                 }
             }
         }

lib/WorkflowMag.groovy

@@ -13,22 +13,18 @@ class WorkflowMag {
     public static void initialise(params, log, hybrid) {
         // Check if binning mapping mode is valid
         if (!['all', 'group', 'own'].contains(params.binning_map_mode)) {
-            log.error "Invalid parameter '--binning_map_mode ${params.binning_map_mode}'. Valid values are 'all', 'group' or 'own'."
-            System.exit(1)
+            Nextflow.error("Invalid parameter '--binning_map_mode ${params.binning_map_mode}'. Valid values are 'all', 'group' or 'own'.")
         }
         if (params.coassemble_group && params.binning_map_mode == 'own') {
-            log.error "Invalid combination of parameter '--binning_map_mode own' and parameter '--coassemble_group'. Select either 'all' or 'group' mapping mode when performing group-wise co-assembly."
-            System.exit(1)
+            Nextflow.error("Invalid combination of parameter '--binning_map_mode own' and parameter '--coassemble_group'. Select either 'all' or 'group' mapping mode when performing group-wise co-assembly.")
         }
 
         // Check if specified cpus for SPAdes are available
         if ( params.spades_fix_cpus > params.max_cpus ) {
-            log.error "Invalid parameter '--spades_fix_cpus ${params.spades_fix_cpus}', max cpus are '${params.max_cpus}'."
-            System.exit(1)
+            Nextflow.error("Invalid parameter '--spades_fix_cpus ${params.spades_fix_cpus}', max cpus are '${params.max_cpus}'.")
         }
         if ( params.spadeshybrid_fix_cpus > params.max_cpus ) {
-            log.error "Invalid parameter '--spadeshybrid_fix_cpus ${params.spadeshybrid_fix_cpus}', max cpus are '${params.max_cpus}'."
-            System.exit(1)
+            Nextflow.error("Invalid parameter '--spadeshybrid_fix_cpus ${params.spadeshybrid_fix_cpus}', max cpus are '${params.max_cpus}'.")
         }
         // Check if settings concerning reproducibility of used tools are consistent and print warning if not
         if (params.megahit_fix_cpu_1 || params.spades_fix_cpus != -1 || params.spadeshybrid_fix_cpus != -1) {
@@ -53,8 +49,7 @@ class WorkflowMag {
 
         // Check if parameters for host contamination removal are valid
         if ( params.host_fasta && params.host_genome) {
-            log.error 'Both host fasta reference and iGenomes genome are specified to remove host contamination! Invalid combination, please specify either --host_fasta or --host_genome.'
-            System.exit(1)
+            Nextflow.error('Both host fasta reference and iGenomes genome are specified to remove host contamination! Invalid combination, please specify either --host_fasta or --host_genome.')
         }
         if ( hybrid && (params.host_fasta || params.host_genome) ) {
             log.warn 'Host read removal is only applied to short reads. Long reads might be filtered indirectly by Filtlong, which is set to use read qualities estimated based on k-mer matches to the short, already filtered reads.'
@@ -64,25 +59,21 @@ class WorkflowMag {
         }
         if ( params.host_genome ) {
             if (!params.genomes) {
-                log.error 'No config file containing genomes provided!'
-                System.exit(1)
+                Nextflow.error('No config file containing genomes provided!')
             }
             // Check if host genome exists in the config file
             if (!params.genomes.containsKey(params.host_genome)) {
-                log.error '=============================================================================\n' +
+                Nextflow.error('=============================================================================\n' +
                         "  Host genome '${params.host_genome}' not found in any config files provided to the pipeline.\n" +
                         '  Currently, the available genome keys are:\n' +
                         "  ${params.genomes.keySet().join(', ')}\n" +
-                        '==================================================================================='
-                System.exit(1)
+                        '===================================================================================')
             }
             if ( !params.genomes[params.host_genome].fasta ) {
-                log.error "No fasta file specified for the host genome ${params.host_genome}!"
-                System.exit(1)
+                Nextflow.error("No fasta file specified for the host genome ${params.host_genome}!")
             }
             if ( !params.genomes[params.host_genome].bowtie2 ) {
-                log.error "No Bowtie 2 index file specified for the host genome ${params.host_genome}!"
-                System.exit(1)
+                Nextflow.error("No Bowtie 2 index file specified for the host genome ${params.host_genome}!")
             }
         }
 
@@ -94,42 +85,34 @@ class WorkflowMag {
         // Check more than one binner is run for bin refinement  (required DAS by Tool)
         // If the number of run binners (i.e., number of not-skipped) is more than one, otherwise throw an error
         if ( params.refine_bins_dastool && !([ params.skip_metabat2, params.skip_maxbin2, params.skip_concoct ].count(false) > 1) ) {
-            log.error 'Bin refinement with --refine_bins_dastool requires at least two binners to be running (not skipped). Check input.'
-            System.exit(1)
+            Nextflow.error('Bin refinement with --refine_bins_dastool requires at least two binners to be running (not skipped). Check input.')
         }
 
         // Check that bin refinement is actually turned on if any of the refined bins are requested for downstream
         if (!params.refine_bins_dastool && params.postbinning_input != 'raw_bins_only') {
-            log.error 'The parameter '--postbinning_input ${ params.postbinning_input }' for downstream steps can only be specified if bin refinement is activated with --refine_bins_dastool! Check input.'
-            System.exit(1)
+            Nextflow.error('The parameter '--postbinning_input ${ params.postbinning_input }' for downstream steps can only be specified if bin refinement is activated with --refine_bins_dastool! Check input.')
         }
 
         // Check if BUSCO parameters combinations are valid
         if (params.skip_binqc && params.binqc_tool == 'checkm') {
-            log.error 'Both --skip_binqc and --binqc_tool \'checkm\' are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool.'
-            System.exit(1)
+            Nextflow.error('Both --skip_binqc and --binqc_tool \'checkm\' are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool.')
         }
         if (params.skip_binqc) {
             if (params.busco_reference) {
-                log.error 'Both --skip_binqc and --busco_reference are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool \'busco\' with --busco_reference.'
-                System.exit(1)
+                Nextflow.error('Both --skip_binqc and --busco_reference are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool \'busco\' with --busco_reference.')
             }
             if (params.busco_download_path) {
-                log.error 'Both --skip_binqc and --busco_download_path are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool \'busco\' with --busco_download_path.'
-                System.exit(1)
+                Nextflow.error('Both --skip_binqc and --busco_download_path are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool \'busco\' with --busco_download_path.')
             }
             if (params.busco_auto_lineage_prok) {
-                log.error 'Both --skip_binqc and --busco_auto_lineage_prok are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool \'busco\' with --busco_auto_lineage_prok.'
-                System.exit(1)
+                Nextflow.error('Both --skip_binqc and --busco_auto_lineage_prok are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool \'busco\' with --busco_auto_lineage_prok.')
             }
         }
         if (params.busco_reference && params.busco_download_path) {
-            log.error 'Both --busco_reference and --busco_download_path are specified! Invalid combination, please specify either --busco_reference or --busco_download_path.'
-            System.exit(1)
+            Nextflow.error('Both --busco_reference and --busco_download_path are specified! Invalid combination, please specify either --busco_reference or --busco_download_path.')
         }
         if (params.busco_auto_lineage_prok && params.busco_reference) {
-            log.error 'Both --busco_auto_lineage_prok and --busco_reference are specified! Invalid combination, please specify either --busco_auto_lineage_prok or --busco_reference.'
-            System.exit(1)
+            Nextflow.error('Both --busco_auto_lineage_prok and --busco_reference are specified! Invalid combination, please specify either --busco_auto_lineage_prok or --busco_reference.')
         }
 
         if (params.skip_binqc && params.gtdb) {
@@ -138,12 +121,10 @@ class WorkflowMag {
 
         // Check if CAT parameters are valid
         if (params.cat_db && params.cat_db_generate) {
-            log.error 'Invalid combination of parameters --cat_db and --cat_db_generate is specified! Please specify either --cat_db or --cat_db_generate.'
-            System.exit(1)
+            Nextflow.error('Invalid combination of parameters --cat_db and --cat_db_generate is specified! Please specify either --cat_db or --cat_db_generate.')
         }
         if (params.save_cat_db && !params.cat_db_generate) {
-            log.error 'Invalid parameter combination: parameter --save_cat_db specified, but not --cat_db_generate! Note also that the parameter --save_cat_db does not work in combination with --cat_db.'
-            System.exit(1)
+            Nextflow.error('Invalid parameter combination: parameter --save_cat_db specified, but not --cat_db_generate! Note also that the parameter --save_cat_db does not work in combination with --cat_db.')
         }
     }
 

workflows/mag.nf

@@ -19,8 +19,7 @@ if(hasExtension(params.input, "csv")){
                 if (row.size() == 5) {
                     if (row.long_reads) hybrid = true
                 } else {
-                    log.error "Input samplesheet contains row with ${row.size()} column(s). Expects 5."
-                    System.exit(1)
+                    Nextflow.error("Input samplesheet contains row with ${row.size()} column(s). Expects 5.")
                 }
             }
 }