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Fix POOL_SHORT_READS receiving reads in wrong roder resulting in faulty pooling #894

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Merged
jfy133 merged 14 commits into from
Nov 17, 2025
Merged

Fix POOL_SHORT_READS receiving reads in wrong roder resulting in faulty pooling #894

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bdf5ac3
Make sure to actually test coassembly
jfy133 Oct 24, 2025
f73c635
Fix input to pooling step to combine reads correctly
jfy133 Oct 25, 2025
dac9ccd
Document fix
jfy133 Oct 25, 2025
24a456b
[automated] Fix code linting
nf-core-bot Oct 25, 2025
b033632
Merge branch 'dev' into 890-metaspades-exit-status-21-paired-read-fil…
jfy133 Oct 28, 2025
12f2b25
Correct version in changelog
jfy133 Oct 28, 2025
0b327d6
Merge branch 'dev' into 890-metaspades-exit-status-21-paired-read-fil…
jfy133 Oct 28, 2025
3cfcb59
Update snapshot to represent pooled (i.e. coassembled) data
jfy133 Oct 28, 2025
66b1301
Merge branch '890-metaspades-exit-status-21-paired-read-files-contain…
jfy133 Oct 28, 2025
13fb75b
Merge branch 'dev' into 890-metaspades-exit-status-21-paired-read-fil…
dialvarezs Nov 16, 2025
4965ca7
Update snapshot
dialvarezs Nov 16, 2025
515f422
Finish fixing of pooling reads
dialvarezs Nov 16, 2025
71af6b1
Update CHANGELOG.md
jfy133 Nov 17, 2025
bb20e9a
Update comment
dialvarezs Nov 17, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#894](https://github.com/nf-core/mag/pull/894) - Fix read order in metaSPAdes to allow co-assembly of paired-end data of multiple samples (reported by @maartenciers, fix by @jfy133 with contributions from @prototaxites, @d4straub and @dialvarezs)
- [#927](https://github.com/nf-core/mag/pull/927) - MetaBinner now succeeds when no contigs are too short or all are binned (reported by @MicroSeq, fix by @d4straub)
- [#929](https://github.com/nf-core/mag/pull/929) - Allow the domain_classification.R script to run with any assembler, not just Megahit or Spades (reported by @MicroSeq, fix by @prototaxites)

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1 change: 1 addition & 0 deletions conf/test_alternatives.config
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Expand Up @@ -27,6 +27,7 @@ params {
// Input data
input = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.v4.csv'
clip_tool = 'trimmomatic'
coassemble_group = true
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d4straub marked this conversation as resolved.
run_busco = true
busco_clean = true
run_checkm2 = true
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25 changes: 17 additions & 8 deletions subworkflows/local/assembly/main.nf
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Expand Up @@ -32,18 +32,27 @@ workflow ASSEMBLY {
.groupTuple(by: 0)
.map { group, metas, reads ->
def assemble_as_single = params.single_end || (params.bbnorm && params.coassemble_group)
def meta = [:]
meta.id = "group-${group}"
meta.group = group
meta.single_end = assemble_as_single
meta.sr_platform = metas.sr_platform[0]
def meta = [
id: "group-${group}",
group: group,
single_end: assemble_as_single,
sr_platform: metas.sr_platform[0]
]
if (assemble_as_single) {
[meta, reads.collect { it }, []]
[meta, reads.collect { file -> file }, []]
}
else {
[meta, reads.collect { it[0] }, reads.collect { it[1] }]
[meta] + reads.sort { files -> files[0].getName() }.transpose()
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}
}

// We have to merge reads together to match tuple structure of POOL_SHORT_READS/
// This MUST be in a interleaved structure (s1_r1, s1_r2, s2_r1, s2_r2, ...)
// So we zip the lists of R1s and R2s, consistent order is ensured by the existing structure
ch_short_reads_grouped_for_pooling = ch_short_reads_grouped.map { meta, reads1, reads2 ->
[meta, [reads1, reads2].transpose().flatten()]
}

// long reads
// group and set group as new id
ch_long_reads_grouped = ch_long_reads
Expand Down Expand Up @@ -73,7 +82,7 @@ workflow ASSEMBLY {
ch_short_reads_spades = ch_short_reads_grouped.map { [it[0], it[1]] }
}
else {
POOL_SHORT_READS(ch_short_reads_grouped)
POOL_SHORT_READS(ch_short_reads_grouped_for_pooling)
ch_versions = ch_versions.mix(POOL_SHORT_READS.out.versions)
ch_short_reads_spades = POOL_SHORT_READS.out.reads
}
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