Merge remote-tracking branch 'upstream/dev' into feat/improve-configs

Author: dialvarezs

CHANGELOG.md

@@ -34,6 +34,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1062](https://github.com/nf-core/mag/pull/1062) - Remove grouping to prevent bin QC blocking by waiting for all binners (by @dialvarezs)
 - [#1063](https://github.com/nf-core/mag/pull/1063) - Run ALE with `--metagenome` and disable its per-base output by default (by @dialvarezs)
 - [#1065](https://github.com/nf-core/mag/pull/1065) - Improved efficiency by removing usage of per-bin GUNZIP module for bins and unbinned contigs and allowing gzip support for all modules (by @dialvarezs)
+- [#1066](https://github.com/nf-core/mag/pull/1066) - Improved efficiency by removing channel "locks" on Seqkit, QUAST, and GTDB-Tk (by @dialvarezs)
+- [#1070](https://github.com/nf-core/mag/pull/1070) - Update BUSCO nf-core module (by @dialvarezs)
 
 ### `Fixed`
 
@@ -47,18 +49,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1031](https://github.com/nf-core/mag/pull/1031) - Fix hybrid co-assembly with SPAdes (short & long reads with `--coassemble_group`) (fix by @d4straub)
 - [#1049](https://github.com/nf-core/mag/pull/1049) - Fix publishing issue with `gtdbtk/classifywf` (by @dialvarezs)
 - [#1058](https://github.com/nf-core/mag/pull/1058) - Make `create_metabinner_bins.py` save gzipped bin files to prevent NFS race condition (by @dialvarezs)
+- [#1069](https://github.com/nf-core/mag/pull/1069) - Exclude eukaryotic bins from CheckM2, which only supports bacterial and archaeal genomes (by @dialvarezs)
 
 ### `Dependencies`
 
 | Tool    | Previous version | New version |
 | ------- | ---------------- | ----------- |
+| BUSCO   | 6.0.0            | 6.1.0       |
 | GTDB-Tk | 2.5.2            | 2.7.2       |
 
 ### `Deprecated`
 
 - [#908](https://github.com/nf-core/mag/pull/908) - Removed local `quast_bins_summary` in favor of `csvtk/concat` (by @dialvarezs)
 - [#1018](https://github.com/nf-core/mag/pull/1018) - Remove `mag_depths_plot` local module (by @dialvarezs)
 - [#1018](https://github.com/nf-core/mag/pull/1018) - Deprecated `--gtdbtk_skip_aniscreen` in favor of `--gtdbtk_place_species` (by @dialvarezs)
+- [#1067](https://github.com/nf-core/mag/pull/1066) - Deprecated `--skip_metaeuk` as it has no effect, MetaEuk is gated by `--metaeuk_db` / `--metaeuk_mmseqs_db` (by @dialvarezs)
 
 ## 5.4.2 Yellow Frog patch [2026-03-31]
 

conf/base.config

@@ -192,4 +192,8 @@ process {
         cpus   = 1
         memory = { 1.GB * task.attempt }
     }
+    withName: SEQKIT_STATS {
+        cpus   = 1
+        memory = { 1.GB * task.attempt }
+    }
 }

conf/containers_conda_lock_files_amd64.config

@@ -1,2 +1,3 @@
+process { withName: 'BUSCO_BUSCO' { container = 'modules/nf-core/busco/busco/.conda-lock/linux_amd64-bd-6d1f7006d91892b3_1.txt' } }
 process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
 process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }

conf/containers_docker_amd64.config

@@ -1,2 +1,3 @@
+process { withName: 'BUSCO_BUSCO' { container = 'community.wave.seqera.io/library/busco:6.1.0--6d1f7006d91892b3' } }
 process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2' } }
 process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }

conf/containers_singularity_https_amd64.config

@@ -1,2 +1,3 @@
+process { withName: 'BUSCO_BUSCO' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/96/963bad66c10646cf0adb1967cc462ad04d02789ddbfae4fbb94182291dbddf8c/data' } }
 process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data' } }
 process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } }

conf/containers_singularity_oras_amd64.config

@@ -1,2 +1,3 @@
+process { withName: 'BUSCO_BUSCO' { container = 'oras://community.wave.seqera.io/library/busco:6.1.0--c7528d5825eb19b5' } }
 process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd' } }
 process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }

conf/modules.config

@@ -1040,6 +1040,8 @@ process {
     }
 
     withName: SEQKIT_STATS {
+        tag        = { "${meta.assembler}-${meta.binner}-${meta.id}" }
+        ext.prefix = { "${meta.assembler}-${meta.binner}-${meta.id}" }
         ext.args   = ""
         maxForks   = params.bin_seqkit_stats_max_forks
         publishDir = [enabled: false]

conf/test_alternatives.config

@@ -50,6 +50,5 @@ params {
     skip_comebin               = true
     skip_metabinner            = true
     skip_semibin               = true
-    skip_metaeuk               = true
     megahit_fix_cpu_1          = true
 }

conf/test_assembly_input.config

@@ -58,7 +58,6 @@ params {
     run_gunc                        = true
     gunc_db                         = params.pipelines_testdata_base_path + 'mag/databases/gunc/ci_test.dmnd'
 
-    skip_metaeuk                    = false
     metaeuk_mmseqs_db               = 'Kalamari'
 }
 

conf/test_longreadonly_alternatives.config

@@ -53,5 +53,4 @@ params {
     skip_comebin                  = true
     skip_metabinner               = true
     skip_semibin                  = true
-    skip_metaeuk                  = true
 }