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Workaround around for CheckM2 database downloading being blocked by Zenodo #966

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Merged
jfy133 merged 2 commits into from
Jan 20, 2026
Merged

Workaround around for CheckM2 database downloading being blocked by Zenodo #966

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Workaround Checkm2 database building until aria2 is unblocked (will r…
jfy133 Jan 20, 2026
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jfy133 Jan 20, 2026
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6 changes: 4 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -7,12 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [965](https://github.com/nf-core/mag/pull/965) - Add support for the generation of custom contig to bin map files for all bins and refined bins (by @jfy133, @prototaxites)
- [965](https://github.com/nf-core/mag/pull/965) - Add support for optional saving of DAS Tool inpout `contig2bin` map files via `--refine_bins_dastool_savecontig2bin`, with now singular generation process (by @jfy133, @prototaxites)
- [#965](https://github.com/nf-core/mag/pull/965) - Add support for the generation of custom contig to bin map files for all bins and refined bins (by @jfy133, @prototaxites)
- [#965](https://github.com/nf-core/mag/pull/965) - Add support for optional saving of DAS Tool inpout `contig2bin` map files via `--refine_bins_dastool_savecontig2bin`, with now singular generation process (by @jfy133, @prototaxites)
- [#963](https://github.com/nf-core/mag/pull/963) - Add support for outputting and median summarising pyDamage results at bin level when running in ancient DNA mode (by @jfy133)

### `Changed`

- [#966](https://github.com/nf-core/mag/pull/966) - Replace aria2c downloading of CheckM2 database with native Nextflow downloading due to Zenodo issues (by @jfy133, @dialvarezs)

### `Fixed`

### `Dependencies`
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -88,7 +88,7 @@
},
"checkm2/predict": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"git_sha": "92c71995da96e0e01946156302997cc86f9324c6",
"installed_by": ["modules"]
},
"chopper": {
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14 changes: 8 additions & 6 deletions modules/nf-core/checkm2/predict/main.nf
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14 changes: 8 additions & 6 deletions modules/nf-core/checkm2/predict/tests/main.nf.test
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15 changes: 11 additions & 4 deletions subworkflows/local/bin_qc/main.nf
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Expand Up @@ -3,7 +3,8 @@
*/

include { BUSCO_BUSCO } from '../../../modules/nf-core/busco/busco/main'
include { CHECKM2_DATABASEDOWNLOAD } from '../../../modules/nf-core/checkm2/databasedownload/main'
// 2016-01-19: Temporarily diabling Checkm2 database downloading due to Zenodo blocking Aria2 downloads
//include { CHECKM2_DATABASEDOWNLOAD } from '../../../modules/nf-core/checkm2/databasedownload/main'
include { CHECKM_QA } from '../../../modules/nf-core/checkm/qa/main'
include { CHECKM_LINEAGEWF } from '../../../modules/nf-core/checkm/lineagewf/main'
include { CHECKM2_PREDICT } from '../../../modules/nf-core/checkm2/predict/main'
Expand All @@ -15,6 +16,7 @@ include { GUNC_RUN } from '../../../modules/nf-core/gunc/ru
include { GUNC_MERGECHECKM } from '../../../modules/nf-core/gunc/mergecheckm/main'
include { UNTAR as BUSCO_UNTAR } from '../../../modules/nf-core/untar/main'
include { UNTAR as CHECKM_UNTAR } from '../../../modules/nf-core/untar/main'
include { UNTAR as CHECKM2_UNTAR } from '../../../modules/nf-core/untar/main'


workflow BIN_QC {
Expand Down Expand Up @@ -63,9 +65,14 @@ workflow BIN_QC {
ch_checkm2_db = [[:], file(params.checkm2_db, checkIfExists: true)]
}
else if (params.run_checkm2) {
CHECKM2_DATABASEDOWNLOAD(params.checkm2_db_version)
ch_versions = ch_versions.mix(CHECKM2_DATABASEDOWNLOAD.out.versions)
ch_checkm2_db = CHECKM2_DATABASEDOWNLOAD.out.database
// 2016-01-19: Temporarily diabling Checkm2 database downloading due to Zenodo blocking Aria2 downloads
//CHECKM2_DATABASEDOWNLOAD(params.checkm2_db_version)
//ch_versions = ch_versions.mix(CHECKM2_DATABASEDOWNLOAD.out.versions)
ch_checkm2_tar = channel.fromPath("https://zenodo.org/records/${params.checkm2_db_version}/files/checkm2_database.tar.gz", checkIfExists: true)
.map { db_tar -> [[id: 'checkm2_db', version: params.checkm2_db_version], db_tar] }
CHECKM2_UNTAR(ch_checkm2_tar)
ch_checkm2_db = CHECKM2_UNTAR.out.untar
ch_versions = ch_versions.mix(CHECKM2_UNTAR.out.versions)
}
else {
ch_checkm2_db = []
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20 changes: 11 additions & 9 deletions tests/test_alternatives.nf.test.snap
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Expand Up @@ -36,12 +36,12 @@
"BUSCO_BUSCO": {
"busco": "6.0.0"
},
"CHECKM2_DATABASEDOWNLOAD": {
"aria2": "1.37.0"
},
"CHECKM2_PREDICT": {
"checkm2": "1.1.0"
},
"CHECKM2_UNTAR": {
"untar": 1.34
},
"CONCAT_BUSCO_TSV": {
"qsv": "5.1.0"
},
Expand Down Expand Up @@ -115,10 +115,10 @@
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nf-test": "0.9.2",
"nextflow": "25.10.2"
},
"timestamp": "2025-11-27T11:32:28.488502608"
"timestamp": "2026-01-20T09:09:31.254713942"
},
"qc": {
"content": [
Expand Down Expand Up @@ -222,6 +222,7 @@
"GenomeBinning/QC/checkm2_summary.tsv",
"GenomeBinning/Tiara/tiara_summary.tsv",
"GenomeBinning/bin_summary.tsv",
"GenomeBinning/contig_to_bin/contig_to_bin_map.tsv",
"GenomeBinning/depths/bins/MEGAHIT-MetaBAT2-group-0-binDepths.heatmap.png",
"GenomeBinning/depths/bins/bin_depths_summary.tsv",
"GenomeBinning/depths/contigs/MEGAHIT-group-0-depth.txt.gz"
Expand All @@ -241,14 +242,15 @@
"checkm2_summary.tsv:md5,ec01903b7f8a7203856a35a7bd2d4c34",
"tiara_summary.tsv:md5,4cbfb0fd90ba48dc33d75d10c1eddb17",
"bin_summary.tsv:md5,cf879345b96d29b5b8584795504b81cf",
"contig_to_bin_map.tsv:md5,2bea485185ed808e9b5568438f603e2a",
"bin_depths_summary.tsv:md5,a73f2fc180a2c52038c88fbbfa6a95c3"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nf-test": "0.9.2",
"nextflow": "25.10.2"
},
"timestamp": "2025-11-28T14:15:43.756748108"
"timestamp": "2026-01-20T09:09:31.818727636"
},
"multiqc": {
"content": [
Expand Down