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Merged
dialvarezs merged 9 commits into from
Nov 17, 2025
Merged

Change deprecated Channel and make closures parameters explicit #932

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8b1e7fd
Change deprecated Channel by channel and use explicit params in closures
dialvarezs Nov 16, 2025
0d18e53
Normalize workflow input type hints
dialvarezs Nov 16, 2025
16f319f
Fix tuple decomposition errors
dialvarezs Nov 16, 2025
00e707f
Remove unneded new line
dialvarezs Nov 16, 2025
f80eddc
Update changelog
dialvarezs Nov 16, 2025
28b481c
Update CHANGELOG.md
dialvarezs Nov 17, 2025
46285e8
Merge remote-tracking branch 'upstream/dev' into fix-deprecations
dialvarezs Nov 17, 2025
65116a9
Add comment for better context
dialvarezs Nov 17, 2025
cbf673e
Sort single end reads too
dialvarezs Nov 17, 2025
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Changed`

- [#932](https://github.com/nf-core/mag/pull/932) - Replaced usages of deprecated `Channel()` with `channel()` and fix other LSP warnings (by @dialvarezs)

### `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)
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6 changes: 3 additions & 3 deletions subworkflows/local/ancient_dna/main.nf
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Expand Up @@ -8,10 +8,10 @@ include { SAMTOOLS_FAIDX as FAIDX } from '../../../modules/nf-core

workflow ANCIENT_DNA_ASSEMBLY_VALIDATION {
take:
ch_input //channel: [val(meta), path(contigs), path(bam), path(bam_index)]
ch_input // [val(meta), path(contigs), path(bam), path(bam_index)]

main:
ch_versions = Channel.empty()
ch_versions = channel.empty()

PYDAMAGE_ANALYZE(
ch_input.map { meta, _contigs, bam, bai ->
Expand All @@ -28,7 +28,7 @@ workflow ANCIENT_DNA_ASSEMBLY_VALIDATION {
ch_versions = ch_versions.mix(PYDAMAGE_FILTER.out.versions)

if (params.skip_ancient_damagecorrection) {
ch_corrected_contigs = Channel.empty()
ch_corrected_contigs = channel.empty()
}

if (!params.skip_ancient_damagecorrection) {
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43 changes: 24 additions & 19 deletions subworkflows/local/assembly/main.nf
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Expand Up @@ -11,12 +11,12 @@ include { GUNZIP as GUNZIP_LONGREAD_ASSEMBLIES } from '../../../modules/nf-core

workflow ASSEMBLY {
take:
ch_short_reads // [ [meta] , fastq1, fastq2] (mandatory)
ch_long_reads // [ [meta] , fastq] (mandatory)
ch_short_reads // [val(meta), path(fastq1), path(fastq2)] (mandatory)
ch_long_reads // [val(meta), path(fastq)] (mandatory)

main:

ch_versions = Channel.empty()
ch_versions = channel.empty()

/*
================================================================================
Expand All @@ -39,7 +39,7 @@ workflow ASSEMBLY {
sr_platform: metas.sr_platform[0]
]
if (assemble_as_single) {
[meta, reads.collect { file -> file }, []]
[meta, reads.sort { files -> files[0].getName() }, []]
}
else {
[meta] + reads.sort { files -> files[0].getName() }.transpose()
Expand All @@ -63,23 +63,28 @@ workflow ASSEMBLY {
meta.id = "group-${group}"
meta.group = group
meta.lr_platform = metas.lr_platform[0]
[meta, reads.collect { it }]
[meta, reads]
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}
}
else {
ch_short_reads_grouped = ch_short_reads
.filter { it[0].single_end }
.map { meta, reads -> [meta, [reads], []] }
.mix(
ch_short_reads.filter { !it[0].single_end }.map { meta, reads -> [meta, [reads[0]], [reads[1]]] }
Comment thread
dialvarezs marked this conversation as resolved.
)
ch_short_reads_grouped = ch_short_reads.map { meta, reads ->
if (meta.single_end) {
[meta, [reads], []]
}
else {
[meta, [reads[0]], [reads[1]]]
}
}

ch_long_reads_grouped = ch_long_reads
}

if (!params.skip_spades || !params.skip_spadeshybrid) {
if (params.coassemble_group) {
if (params.bbnorm) {
ch_short_reads_spades = ch_short_reads_grouped.map { [it[0], it[1]] }
// When doing co-assembly and using bbnorm, all sample reads get pooled in a single file
// That's why we can drop R2 here (it's empty)
ch_short_reads_spades = ch_short_reads_grouped.map { meta, r1, _r2 -> [meta, r1] }
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}
else {
POOL_SHORT_READS(ch_short_reads_grouped_for_pooling)
Expand All @@ -95,21 +100,21 @@ workflow ASSEMBLY {

ch_long_reads_grouped_for_pool = ch_long_reads_grouped
.map { meta, reads -> [meta.id, meta, reads] }
.combine(ch_short_reads_grouped.map { meta, _reads1, _reads2 -> [meta.id, meta] }, by: 0)
.map { [it[1], it[2]] }
.combine(ch_short_reads_grouped.map { meta, _reads1, _reads2 -> [meta.id] }, by: 0)
.map { _id, lr_meta, lr_reads -> [lr_meta, lr_reads] }
//make sure no long reads are pooled for spades if there are no short reads

POOL_LONG_READS(ch_long_reads_grouped_for_pool)
ch_versions = ch_versions.mix(POOL_LONG_READS.out.versions)
ch_long_reads_spades = POOL_LONG_READS.out.reads
}
else {
ch_long_reads_spades = Channel.empty()
ch_long_reads_spades = channel.empty()
}
}
else {
ch_short_reads_spades = Channel.empty()
ch_long_reads_spades = Channel.empty()
ch_short_reads_spades = channel.empty()
ch_long_reads_spades = channel.empty()
}

/*
Expand All @@ -118,8 +123,8 @@ workflow ASSEMBLY {
================================================================================
*/

ch_shortread_assembled_contigs = Channel.empty()
ch_longread_assembled_contigs = Channel.empty()
ch_shortread_assembled_contigs = channel.empty()
ch_longread_assembled_contigs = channel.empty()

// SHORTREAD ASSEMBLY
SHORTREAD_ASSEMBLY(
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8 changes: 4 additions & 4 deletions subworkflows/local/assembly_hybrid/main.nf
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Expand Up @@ -3,13 +3,13 @@ include { SPADES as METASPADESHYBRID } from '../../../modules/nf-core/spades/mai

workflow HYBRID_ASSEMBLY {
take:
ch_short_reads_spades // [ [meta] , fastq1, fastq2] (mandatory)
ch_long_reads_spades // [ [meta] , fastq] (mandatory)
ch_short_reads_spades // [val(meta), path(fastq1), path(fastq2)] (mandatory)
ch_long_reads_spades // [val(meta), path(fastq)] (mandatory)

main:

ch_versions = Channel.empty()
ch_assembled_contigs = Channel.empty()
ch_versions = channel.empty()
ch_assembled_contigs = channel.empty()

if (!params.single_end && !params.skip_spadeshybrid) {
ch_short_reads_spades_tmp = ch_short_reads_spades.map { meta, reads -> [meta.id, meta, reads] }
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6 changes: 3 additions & 3 deletions subworkflows/local/assembly_longread/main.nf
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Expand Up @@ -7,11 +7,11 @@ include { METAMDBG_ASM } from '../../../modules/nf-core/metamdbg/asm/main'

workflow LONGREAD_ASSEMBLY {
take:
ch_long_reads // [ [meta] , fastq] (mandatory)
ch_long_reads // [val(meta), path(fastq)] (mandatory)

main:
ch_assembled_contigs = Channel.empty()
ch_versions = Channel.empty()
ch_assembled_contigs = channel.empty()
ch_versions = channel.empty()

if (!params.skip_flye) {

Expand Down
8 changes: 4 additions & 4 deletions subworkflows/local/assembly_shortread/main.nf
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Expand Up @@ -4,12 +4,12 @@ include { SPADES as METASPADES } from '../../../modules/nf-core/spades/main'

workflow SHORTREAD_ASSEMBLY {
take:
ch_short_reads_grouped // [ [meta] , fastq1, fastq2] (mandatory)
ch_short_reads_spades
ch_short_reads_grouped // [val(meta), path(fastq1), path(fastq2)] (mandatory)
ch_short_reads_spades // [val(meta), path(fastq1)] (mandatory)

main:
ch_versions = Channel.empty()
ch_assembled_contigs = Channel.empty()
ch_versions = channel.empty()
ch_assembled_contigs = channel.empty()

if (!params.single_end && !params.skip_spades) {
METASPADES(ch_short_reads_spades.map { meta, reads -> [meta, reads, [], []] }, [], [])
Expand Down
56 changes: 37 additions & 19 deletions subworkflows/local/bin_qc/main.nf
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Expand Up @@ -19,16 +19,16 @@ include { UNTAR as CHECKM_UNTAR } from '../../../modules/nf-core/un

workflow BIN_QC {
take:
ch_bins // [ [ meta] , fasta ], input bins (mandatory)
ch_bins // [val(meta), path(fasta)], input bins (mandatory)

main:
ch_qc_summaries = Channel.empty()
ch_qc_summaries = channel.empty()
ch_input_bins_for_qc = ch_bins.transpose()
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
ch_busco_final_summaries = Channel.empty()
ch_checkm_final_summaries = Channel.empty()
ch_checkm2_final_summaries = Channel.empty()
ch_versions = channel.empty()
ch_multiqc_files = channel.empty()
ch_busco_final_summaries = channel.empty()
ch_checkm_final_summaries = channel.empty()
ch_checkm2_final_summaries = channel.empty()


/*
Expand All @@ -53,7 +53,7 @@ workflow BIN_QC {
CHECKM_UNTAR(ch_checkm_db)
ch_versions = ch_versions.mix(CHECKM_UNTAR.out.versions)

ch_checkm_db = CHECKM_UNTAR.out.untar.map { it[1] }
ch_checkm_db = CHECKM_UNTAR.out.untar.map { _meta, db -> db }
}
else {
ch_checkm_db = []
Expand All @@ -75,7 +75,7 @@ workflow BIN_QC {
ch_gunc_db = file(params.gunc_db, checkIfExists: true)
}
else {
ch_gunc_db = Channel.empty()
ch_gunc_db = channel.empty()
}

/*
Expand All @@ -93,7 +93,7 @@ workflow BIN_QC {
if (ch_busco_db && ch_busco_db.extension in ['gz', 'tgz']) {
BUSCO_UNTAR([[id: ch_busco_db.getSimpleName()], ch_busco_db])
ch_versions = ch_versions.mix(BUSCO_UNTAR.out.versions)
ch_busco_db = BUSCO_UNTAR.out.untar.map { it[1] }
ch_busco_db = BUSCO_UNTAR.out.untar.map { _meta, db -> db }
}
else if (ch_busco_db && ch_busco_db.isDirectory()) {
ch_busco_db = ch_busco_db
Expand All @@ -109,13 +109,19 @@ workflow BIN_QC {
.map { _meta, summary -> [[id: 'busco'], summary] }
.groupTuple()
ch_multiqc_files = ch_multiqc_files.mix(
BUSCO_BUSCO.out.short_summaries_txt.map { it[1] }.flatten()
BUSCO_BUSCO.out.short_summaries_txt.map { _meta, summary -> summary }.flatten()
)

CONCAT_BUSCO_TSV(ch_busco_summaries, 'tsv', 'tsv')
ch_versions = ch_versions.mix(CONCAT_BUSCO_TSV.out.versions)
ch_busco_final_summaries = ch_busco_final_summaries.mix(CONCAT_BUSCO_TSV.out.csv.map { it[1] })
ch_qc_summaries = ch_qc_summaries.mix(CONCAT_BUSCO_TSV.out.csv.splitCsv(header: true, sep: '\t').map { _meta, summary -> [bin_qc_tool: 'busco'] + summary })
ch_busco_final_summaries = ch_busco_final_summaries.mix(
CONCAT_BUSCO_TSV.out.csv.map { _meta, csv -> csv }
)
ch_qc_summaries = ch_qc_summaries.mix(
CONCAT_BUSCO_TSV.out.csv
.splitCsv(header: true, sep: '\t')
.map { _meta, summary -> [bin_qc_tool: 'busco'] + summary }
)
}
if (params.run_checkm) {
/*
Expand Down Expand Up @@ -147,13 +153,19 @@ workflow BIN_QC {
.map { _meta, summary -> [[id: 'checkm'], summary] }
.groupTuple()
ch_multiqc_files = ch_multiqc_files.mix(
CHECKM_QA.out.output.map { it[1] }.flatten()
CHECKM_QA.out.output.map { _meta, summary -> summary }.flatten()
)

CONCAT_CHECKM_TSV(ch_checkm_summaries, 'tsv', 'tsv')
ch_versions = ch_versions.mix(CONCAT_CHECKM_TSV.out.versions)
ch_checkm_final_summaries = ch_checkm_final_summaries.mix(CONCAT_CHECKM_TSV.out.csv.map { it[1] })
ch_qc_summaries = ch_qc_summaries.mix(CONCAT_CHECKM_TSV.out.csv.splitCsv(header: true, sep: '\t').map { _meta, summary -> [bin_qc_tool: 'checkm'] + summary })
ch_checkm_final_summaries = ch_checkm_final_summaries.mix(
CONCAT_CHECKM_TSV.out.csv.map { _meta, csv -> csv }
)
ch_qc_summaries = ch_qc_summaries.mix(
CONCAT_CHECKM_TSV.out.csv
.splitCsv(header: true, sep: '\t')
.map { _meta, summary -> [bin_qc_tool: 'checkm'] + summary }
)
}
if (params.run_checkm2) {
/*
Expand All @@ -166,13 +178,19 @@ workflow BIN_QC {
.map { _meta, summary -> [[id: 'checkm2'], summary] }
.groupTuple()
ch_multiqc_files = ch_multiqc_files.mix(
CHECKM2_PREDICT.out.checkm2_tsv.map { it[1] }.flatten()
CHECKM2_PREDICT.out.checkm2_tsv.map { _meta, summary -> summary }.flatten()
)

CONCAT_CHECKM2_TSV(ch_checkm2_summaries, 'tsv', 'tsv')
ch_versions = ch_versions.mix(CONCAT_CHECKM2_TSV.out.versions)
ch_checkm2_final_summaries = ch_checkm2_final_summaries.mix(CONCAT_CHECKM2_TSV.out.csv.map { it[1] })
ch_qc_summaries = ch_qc_summaries.mix(CONCAT_CHECKM2_TSV.out.csv.splitCsv(header: true, sep: '\t').map { _meta, summary -> [bin_qc_tool: 'checkm2'] + summary })
ch_checkm2_final_summaries = ch_checkm2_final_summaries.mix(
CONCAT_CHECKM2_TSV.out.csv.map { _meta, csv -> csv }
)
ch_qc_summaries = ch_qc_summaries.mix(
CONCAT_CHECKM2_TSV.out.csv
.splitCsv(header: true, sep: '\t')
.map { _meta, summary -> [bin_qc_tool: 'checkm2'] + summary }
)
}

if (params.run_gunc) {
Expand Down
30 changes: 16 additions & 14 deletions subworkflows/local/binning/main.nf
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Expand Up @@ -20,22 +20,22 @@ include { SPLIT_FASTA

workflow BINNING {
take:
ch_assemblies // channel: [ val(meta), path(assembly), path(bams), path(bais) ]
val_bin_min_size
val_bin_max_size
ch_assemblies // [val(meta), path(assembly), path(bams), path(bais)]
val_bin_min_size // val(int)
val_bin_max_size // val(int)

main:

ch_versions = Channel.empty()
ch_input_splitfasta = Channel.empty()
ch_versions = channel.empty()
ch_input_splitfasta = channel.empty()

// generate coverage depths for each contig and branch by assembler type
ch_summarizedepth_input = ch_assemblies
.map { meta, _assembly, bams, bais ->
[meta, bams, bais]
}
.branch {
longread: it[0].assembler in ['FLYE', 'METAMDBG']
.branch { meta, _bams, _bais ->
longread: meta.assembler in ['FLYE', 'METAMDBG']
shortread: true
}

Expand All @@ -47,7 +47,9 @@ workflow BINNING {
ch_versions = ch_versions.mix(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD.out.versions)

// Merge the outputs
ch_combined_depths = METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD.out.depth.mix(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD.out.depth)
ch_combined_depths = METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD.out.depth.mix(
METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD.out.depth
)
ch_metabat_depths = ch_combined_depths.map { meta, depths ->
def meta_new = meta + [binner: 'MetaBAT2']
[meta_new, depths]
Expand Down Expand Up @@ -76,10 +78,10 @@ workflow BINNING {
}

// main bins for decompressing for MAG_DEPTHS
ch_bins_for_seqkit = Channel.empty()
ch_bins_for_seqkit = channel.empty()

// final gzipped bins
ch_binning_results_gzipped_final = Channel.empty()
ch_binning_results_gzipped_final = channel.empty()

// MetaBAT2
if (!params.skip_metabat2) {
Expand Down Expand Up @@ -128,7 +130,7 @@ workflow BINNING {
// COMEBin
if (!params.skip_comebin) {
ch_comebin_input = ch_assemblies
.map { meta, assembly, bams, bais ->
.map { meta, assembly, bams, _bais ->
def meta_new = meta + [binner: 'COMEBin']
[meta_new, assembly, bams]
}
Expand Down Expand Up @@ -179,12 +181,12 @@ workflow BINNING {
// filtering is 0. Error if so, but only if we had bins to begin with.
//
ch_seqkitstats_results
.map { meta, stats -> stats.bin_total_length }
.map { _meta, stats -> stats.bin_total_length }
.collect().ifEmpty([])
.subscribe { stats ->
def n_bins = stats.size()
def n_filtered_bins = stats.findAll {
it >= val_bin_min_size && (val_bin_max_size ? it <= val_bin_max_size : true)
def n_filtered_bins = stats.findAll { bin_size ->
bin_size >= val_bin_min_size && (val_bin_max_size ? bin_size <= val_bin_max_size : true)
}.size()
if (n_bins > 0 && n_filtered_bins == 0) {
error(
Expand Down
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