diff --git a/CHANGELOG.md b/CHANGELOG.md index feb3c137..9e0d2429 100644 --- a/CHANGELOG.md +++ b/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` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index de0b96a6..234d1d8d 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/mag + This report has been generated by the nf-core/mag analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-mag-methods-description": order: -1000 diff --git a/conf/test_full.config b/conf/test_full.config index ea694247..d7f3365e 100644 --- a/conf/test_full.config +++ b/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 diff --git a/nextflow.config b/nextflow.config index fd0094b9..6a2da3b5 100644 --- a/nextflow.config +++ b/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' } diff --git a/workflows/mag.nf b/workflows/mag.nf index 61ce43bc..6ec7b132 100644 --- a/workflows/mag.nf +++ b/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() }