Merge pull request #577 from nf-core/dev

2.5.3 patch release

CHANGELOG.md

@@ -3,6 +3,22 @@
 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).
 
+## 2.5.3 - [2024-02-05]
+
+### `Added`
+
+### `Changed`
+
+- [#575](https://github.com/nf-core/mag/pull/575) - Deactivated MetaSPAdes, Centrifuge, and GTDB in test_full profile due to some container incompatibilities in nf-core megatest AWS configurations (by @jfy133)
+
+### `Fixed`
+
+- [#574](https://github.com/nf-core/mag/pull/574) - Fix wrong channel going to BIN_SUMMARY (fix by @maxibor)
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## 2.5.2 - [2024-02-02]
 
 ### `Added`

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/releases/tag/2.5.2" target="_blank">nf-core/mag</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/2.5.3" 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/2.5.2/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/2.5.3/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000

conf/test_full.config

@@ -19,15 +19,21 @@ params {
     host_fasta    = "s3://ngi-igenomes/test-data/mag/hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz"
     input         = "s3://ngi-igenomes/test-data/mag/samplesheets/samplesheet.full.csv"
 
-    centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz"
+    //centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz"
     kraken2_db    = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz"
     cat_db        = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz"
-    gtdb_db       = "s3://ngi-igenomes/test-data/mag/gtdbtk_r202_data.tar.gz"
+    // gtdb_db       = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz"
+    skip_gtdbtk   = true
+
+    // TODO TEMPORARY: deactivate SPAdes due to incompatibility of container with fusion file system
+    skip_spades       = true
+    skip_spadeshybrid = true
 
     // reproducibility options for assembly
     spades_fix_cpus       = 10
     spadeshybrid_fix_cpus = 10
     megahit_fix_cpu_1     = true
+
     // available options to enable reproducibility for BUSCO (--busco_db) not used here
     // to allow detection of possible problems in automated lineage selection mode using public databases
 

nextflow.config

@@ -379,7 +379,7 @@ manifest {
     description     = """Assembly, binning and annotation of metagenomes"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.5.2'
+    version         = '2.5.3'
     doi             = '10.1093/nargab/lqac007'
 }
 

workflows/mag.nf

@@ -960,7 +960,7 @@ workflow MAG {
 
         // If CAT is not run, then the CAT global summary should be an empty channel
         if ( params.cat_db_generate || params.cat_db) {
-            ch_cat_global_summary = CAT_SUMMARY.out.summary
+            ch_cat_global_summary = CAT_SUMMARY.out.combined
         } else {
             ch_cat_global_summary = Channel.empty()
         }