Merge pull request #442 from nf-core/busco-warn-removal [skip ci]

Remove BUSCO warning about no matches found

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#428](https://github.com/nf-core/mag/pull/428) - Update to nf-core 2.8 `TEMPLATE` (by @jfy133)
 - [#429](https://github.com/nf-core/mag/pull/429) - Replaced hardcoded CheckM database auto-download URL to a parameter (reported by @erikrikarddaniel, fix by @jfy133)
 - [#441](https://github.com/nf-core/mag/pull/441) - Deactivated CONCOCT in AWS 'full test' due to very long runtime (fix by @jfy133).
+- [#442](https://github.com/nf-core/mag/pull/442) - Remove warning when BUSCO finds no genes in bins, as this can be expected in some datasets (reported by @Lumimar, fix by @jfy133).
 
 ### `Fixed`
 

lib/NfcoreTemplate.groovy

@@ -58,9 +58,7 @@ class NfcoreTemplate {
 
         // Set up the e-mail variables
         def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
-        if (busco_failed_bins.size() > 0) {
-            subject = "[$workflow.manifest.name] Partially successful: For ${busco_failed_bins.size()} bin(s) the BUSCO analysis failed because no genes where found or placements failed: $workflow.runName"
-        }
+
         if (!workflow.success) {
             subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
         }
@@ -231,32 +229,6 @@ class NfcoreTemplate {
     //
     public static void summary(workflow, params, log, busco_failed_bins = [:]) {
         Map colors = logColours(params.monochrome_logs)
-
-        if (busco_failed_bins.size() > 0) {
-            def failed_bins_no_genes = ''
-            def failed_bins_placements_failed = ''
-            def count_no_genes = 0
-            def count_placements_failed = 0
-            for (bin in busco_failed_bins) {
-                if (bin.value == "No genes"){
-                    count_no_genes += 1
-                    failed_bins_no_genes += "    ${bin.key}\n"
-                }
-                if (bin.value == "Placements failed"){
-                    count_placements_failed += 1
-                    failed_bins_placements_failed += "    ${bin.key}\n"
-                }
-            }
-            if (params.busco_reference)
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} For ${busco_failed_bins.size()} bin(s) BUSCO did not find any matching genes:\n${failed_bins_no_genes}See ${params.outdir}/GenomeBinning/QC/BUSCO/[bin]_busco.log for further information.${colors.reset}-"
-            else {
-                if (count_no_genes > 0)
-                    log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} For ${count_no_genes} bin(s) the BUSCO analysis failed because no BUSCO genes could be found:\n${failed_bins_no_genes}See ${params.outdir}/GenomeBinning/QC/BUSCO/[bin]_busco.err and ${params.outdir}/GenomeBinning/QC/BUSCO/[bin]_busco.log for further information.${colors.reset}-"
-                if (count_placements_failed > 0)
-                    log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} For ${count_placements_failed} bin(s) the BUSCO analysis using automated lineage selection failed due to failed placements:\n${failed_bins_placements_failed}See ${params.outdir}/GenomeBinning/QC/BUSCO/[bin]_busco.err and ${params.outdir}/GenomeBinning/QC/BUSCO/[bin]_busco.log for further information. Results for selected domain are still used.${colors.reset}-"
-            }
-        }
-
         if (workflow.success) {
             if (workflow.stats.ignoredCount == 0) {
                 log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"