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add missing channels for workflow outputs #10918

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Merged
atrigila merged 2 commits into from
Mar 16, 2026
Merged

add missing channels for workflow outputs #10918

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f704e55
add missing channels for workflow outputs
atrigila Mar 16, 2026
15a4611
collect bcl2fastq undetermined
atrigila Mar 16, 2026
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22 changes: 13 additions & 9 deletions subworkflows/nf-core/bcl_demultiplex/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ workflow BCL_DEMULTIPLEX {
ch_interop = channel.empty()
ch_logs = channel.empty()
ch_sav_files = channel.empty()
ch_undetermined = channel.empty()

// MODULE: bclconvert
// Demultiplex the bcl files
Expand All @@ -28,6 +29,7 @@ workflow BCL_DEMULTIPLEX {
ch_interop = ch_interop.mix(BCLCONVERT.out.interop)
ch_reports = ch_reports.mix(BCLCONVERT.out.reports)
ch_logs = ch_logs.mix(BCLCONVERT.out.logs)
ch_undetermined = ch_undetermined.mix(BCLCONVERT.out.undetermined)
ch_sav_files = ch_sav_files.mix(BCLCONVERT.out.reports)
ch_fastq_with_meta = ch_fastq_with_meta.mix(
generateReadgroupBCLCONVERT(
Expand All @@ -46,6 +48,7 @@ workflow BCL_DEMULTIPLEX {
ch_interop = ch_interop.mix(BCL2FASTQ.out.interop)
ch_reports = ch_reports.mix(BCL2FASTQ.out.reports)
ch_stats = ch_stats.mix(BCL2FASTQ.out.stats)
ch_undetermined = ch_undetermined.mix(BCL2FASTQ.out.undetermined)
ch_sav_files = ch_sav_files.mix(BCL2FASTQ.out.stats)
ch_fastq_with_meta = ch_fastq_with_meta.mix(
generateReadgroupBCL2FASTQ(
Expand Down Expand Up @@ -83,15 +86,16 @@ workflow BCL_DEMULTIPLEX {
}

emit:
fastq = ch_fastq.fastq
empty_fastq = ch_fastq.empty
reports = ch_reports
stats = ch_stats
interop = ch_interop
logs = ch_logs
sav_report = MULTIQCSAV.out.report
sav_data = MULTIQCSAV.out.data
sav_plots = MULTIQCSAV.out.plots
fastq = ch_fastq.fastq
empty_fastq = ch_fastq.empty
reports = ch_reports
stats = ch_stats
interop = ch_interop
logs = ch_logs
undetermined = ch_undetermined
sav_report = MULTIQCSAV.out.report
sav_data = MULTIQCSAV.out.data
sav_plots = MULTIQCSAV.out.plots
}

def generateReadgroupBCLCONVERT(ch_fastq_list_csv, ch_fastq) {
Expand Down
4 changes: 2 additions & 2 deletions subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "sav_report", "sav_data", "sav_plots"]).collectEntries { key, val ->
sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "sav_report", "sav_data", "sav_plots", "undetermined"]).collectEntries { key, val ->
if (key == "interop") {
return [ key, val.collect { meta, files ->
[
Expand Down Expand Up @@ -93,7 +93,7 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "sav_report", "sav_data", "sav_plots"]).collectEntries { key, val ->
sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "sav_report", "sav_data", "sav_plots", "undetermined"]).collectEntries { key, val ->
if (key == "fastq")
if (key == "interop") {
return [ key, val.collect { meta, files ->
Expand Down
24 changes: 18 additions & 6 deletions subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -170,14 +170,23 @@
],
"stats": [

],
"undetermined": [
[
{
"id": "HMTFYDRXX",
"lane": 1
},
"Undetermined_S0_L001_R1_001.fastq.gz"
]
]
}
],
"timestamp": "2026-03-16T13:47:40.083238326",
"meta": {
"nf-test": "0.9.3",
"nf-test": "0.9.4",
"nextflow": "25.10.4"
},
"timestamp": "2026-03-04T19:55:51.054792"
}
},
"bcl2fastq": {
"content": [
Expand Down Expand Up @@ -309,13 +318,16 @@
"Stats.json:md5,8e5f038b8aa9e465599d3575f930e604"
]
]
],
"undetermined": [

]
}
],
"timestamp": "2026-03-16T13:48:09.325036018",
"meta": {
"nf-test": "0.9.3",
"nf-test": "0.9.4",
"nextflow": "25.10.4"
},
"timestamp": "2026-03-04T19:42:28.852443"
}
}
}
3 changes: 2 additions & 1 deletion subworkflows/nf-core/fastq_contam_seqtk_kraken/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -39,5 +39,6 @@ workflow FASTQ_CONTAM_SEQTK_KRAKEN {
ch_reports = ch_reports.mix(KRAKEN2.out.report)

emit:
reports = ch_reports // channel: [ [meta], log ]
reports = ch_reports // channel: [ [meta], log ]
reads = SEQTK_SAMPLE.out.reads // channel: [ [meta], reads ]
}
120 changes: 106 additions & 14 deletions subworkflows/nf-core/fastq_contam_seqtk_kraken/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,42 @@
"test.25000.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
]
],
"1": [
[
{
"id": "test",
"single_end": true,
"n_reads": 12500
},
"test.12500_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
],
[
{
"id": "test",
"single_end": true,
"n_reads": 25000
},
"test.25000_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
]
],
"reads": [
[
{
"id": "test",
"single_end": true,
"n_reads": 12500
},
"test.12500_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
],
[
{
"id": "test",
"single_end": true,
"n_reads": 25000
},
"test.25000_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
]
],
"reports": [
[
{
Expand All @@ -40,11 +76,11 @@
]
}
],
"timestamp": "2026-03-16T13:43:30.024469728",
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.10.2"
},
"timestamp": "2026-01-15T17:23:21.150863294"
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
},
"sarscov2 - fastq - [12500, 25000] - krakendb -- stub": {
"content": [
Expand All @@ -67,6 +103,42 @@
"test.25000.kraken2.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test",
"single_end": true,
"n_reads": 12500
},
"test.12500.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
],
[
{
"id": "test",
"single_end": true,
"n_reads": 25000
},
"test.25000.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"reads": [
[
{
"id": "test",
"single_end": true,
"n_reads": 12500
},
"test.12500.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
],
[
{
"id": "test",
"single_end": true,
"n_reads": 25000
},
"test.25000.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"reports": [
[
{
Expand All @@ -87,14 +159,14 @@
]
},
[

]
],
"timestamp": "2026-03-16T13:43:39.839595283",
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.10.2"
},
"timestamp": "2026-01-15T17:23:31.030729105"
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
},
"sarscov2 - fastq - 25000 - krakendb": {
"content": [
Expand All @@ -109,6 +181,26 @@
"test.25000.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
]
],
"1": [
[
{
"id": "test",
"single_end": true,
"n_reads": 25000
},
"test.25000_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
]
],
"reads": [
[
{
"id": "test",
"single_end": true,
"n_reads": 25000
},
"test.25000_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
]
],
"reports": [
[
{
Expand All @@ -121,10 +213,10 @@
]
}
],
"timestamp": "2026-03-16T13:43:20.617712027",
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.10.2"
},
"timestamp": "2026-01-15T17:23:10.743490624"
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
}
}
}
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