2.4 release version bump

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 2.4.0dev - [date]
+## 2.4.0 - 2023-09-07
 
 ### `Added`
 
@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#444](https://github.com/nf-core/mag/pull/444) - Moved BUSCO bash code to script (by @jfy133)
 - [#428](https://github.com/nf-core/mag/pull/429) - Update to nf-core 2.9 `TEMPLATE` (by @jfy133)
 - [#437](https://github.com/nf-core/mag/pull/429) - `--gtdb` parameter is split into `--skip_gtdbtk` and `--gtdb_db` to allow finer control over GTDB database retrieval (fix by @jfy133)
+- [#500](https://github.com/nf-core/mag/pull/500) - Temporarily disabled downstream processing of both refined and raw bins due to bug (by @jfy133)
 
 ### `Fixed`
 
@@ -41,6 +42,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#470](https://github.com/nf-core/mag/pull/470) - Fix binning preparation from running even when binning was requested to be skipped (reported by @prototaxites, fix by @jfy133)
 - [#480](https://github.com/nf-core/mag/pull/480) - Improved `-resume` reliability through better meta map preservation (reported by @prototaxites, fix by @jfy133)
 - [#493](https://github.com/nf-core/mag/pull/493) - Update `METABAT2` nf-core module so that it reduced the number of unnecessary file moves, enabling virtual filesystems (fix by @adamrtalbot)
+- [#500](https://github.com/nf-core/mag/pull/500) - Fix MaxBin2 bins not being saved in results directly properly (reported by @Perugolate, fix by @jfy133)
 
 ### `Dependencies`
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mag/2.4.0dev" target="_blank">nf-core/mag</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mag/2.4.0" target="_blank">nf-core/mag</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mag/2.4.0dev/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/2.4.0/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000

conf/modules.config

@@ -621,7 +621,7 @@ process {
             [
                 path: { "${params.outdir}/GenomeBinning/MaxBin2/bins/" },
                 mode: params.publish_dir_mode,
-                pattern: '*/*.fa.gz'
+                pattern: '*.fa.gz'
             ],
         ]
     }

conf/test_binrefinement.config

@@ -31,6 +31,7 @@ params {
     skip_gtdbtk                   = true
     refine_bins_dastool           = true
     refine_bins_dastool_threshold = 0
-    postbinning_input             = 'both'
+    // TODO not using 'both' until #489 merged
+    postbinning_input             = 'refined_bins_only'
     busco_clean                   = true
 }

nextflow.config

@@ -371,7 +371,7 @@ manifest {
     description     = """Assembly, binning and annotation of metagenomes"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.4.0dev'
+    version = '2.4.0'
     doi             = '10.1093/nargab/lqac007'
 }
 

nextflow_schema.json

@@ -522,23 +522,23 @@
                 },
                 "gtdbtk_min_completeness": {
                     "type": "number",
-                    "default": 50,
+                    "default": 50.0,
                     "description": "Min. bin completeness (in %) required to apply GTDB-tk classification.",
                     "help_text": "Completeness assessed with BUSCO analysis (100% - %Missing). Must be greater than 0 (min. 0.01) to avoid GTDB-tk errors. If too low, GTDB-tk classification results can be impaired due to not enough marker genes!",
                     "minimum": 0.01,
                     "maximum": 100
                 },
                 "gtdbtk_max_contamination": {
                     "type": "number",
-                    "default": 10,
+                    "default": 10.0,
                     "description": "Max. bin contamination (in %) allowed to apply GTDB-tk classification.",
                     "help_text": "Contamination approximated based on BUSCO analysis (%Complete and duplicated). If too high, GTDB-tk classification results can be impaired due to contamination!",
                     "minimum": 0,
                     "maximum": 100
                 },
                 "gtdbtk_min_perc_aa": {
                     "type": "number",
-                    "default": 10,
+                    "default": 10.0,
                     "description": "Min. fraction of AA (in %) in the MSA for bins to be kept.",
                     "minimum": 0,
                     "maximum": 100
@@ -552,7 +552,7 @@
                 },
                 "gtdbtk_pplacer_cpus": {
                     "type": "number",
-                    "default": 1,
+                    "default": 1.0,
                     "description": "Number of CPUs used for the by GTDB-Tk run tool pplacer.",
                     "help_text": "A low number of CPUs helps to reduce the memory required/reported by GTDB-Tk. See also the [GTDB-Tk documentation](https://ecogenomics.github.io/GTDBTk/faq.html#gtdb-tk-reaches-the-memory-limit-pplacer-crashes)."
                 },
@@ -807,8 +807,8 @@
                     "type": "string",
                     "default": "raw_bins_only",
                     "description": "Specify which binning output is sent for downstream annotation, taxonomic classification, bin quality control etc.",
-                    "help_text": "`raw_bins_only`: only bins (and unbinned contigs) from the binners.\n`refined_bins_only`:  only bins (and unbinned contigs) from the bin refinement step .\n`both`: bins and unbinned contigs from both the binning and bin refinement steps.",
-                    "enum": ["raw_bins_only", "refined_bins_only", "both"]
+                    "help_text": "`raw_bins_only`: only bins (and unbinned contigs) from the binners.\n`refined_bins_only`:  only bins (and unbinned contigs) from the bin refinement step .\n\n ~~`both`: bins and unbinned contigs from both the binning and bin refinement steps.~~ `both` option is disabled in v2.4 due a bug that will be fixed in a later release.",
+                    "enum": ["raw_bins_only", "refined_bins_only"]
                 },
                 "run_gunc": {
                     "type": "boolean",

workflows/mag.nf

@@ -765,10 +765,12 @@ workflow MAG {
             } else if ( params.postbinning_input == 'refined_bins_only' ) {
                 ch_input_for_postbinning_bins        = ch_refined_bins
                 ch_input_for_postbinning_bins_unbins = ch_refined_bins.mix(ch_refined_unbins)
-            } else if ( params.postbinning_input == 'both' ) {
-                ch_all_bins = ch_binning_results_bins.mix(ch_refined_bins)
-                ch_input_for_postbinning_bins        = ch_all_bins
-                ch_input_for_postbinning_bins_unbins = ch_all_bins.mix(ch_binning_results_unbins).mix(ch_refined_unbins)
+            // TODO REACTIVATE ONCE PR #489 IS READY!
+            // TODO RE-ADD BOTH TO SCHEMA ONCE RE-ADDING
+            // } else if ( params.postbinning_input == 'both' ) {
+            //     ch_all_bins = ch_binning_results_bins.mix(ch_refined_bins)
+            //     ch_input_for_postbinning_bins        = ch_all_bins
+            //     ch_input_for_postbinning_bins_unbins = ch_all_bins.mix(ch_binning_results_unbins).mix(ch_refined_unbins)
             }
         } else {
             ch_input_for_postbinning_bins        = ch_binning_results_bins