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Merge pull request #577 from nf-core/dev
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2.5.3 patch release
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jfy133 authored Feb 5, 2024
2 parents 274412a + 532a7c7 commit 7bd5dc6
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16 changes: 16 additions & 0 deletions CHANGELOG.md
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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`
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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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@@ -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
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10 changes: 8 additions & 2 deletions conf/test_full.config
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -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'
}

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2 changes: 1 addition & 1 deletion workflows/mag.nf
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Expand Up @@ -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()
}
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