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atrigilaatrigila
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add missing channels for workflow outputs (#10918)
* add missing channels for workflow outputs * collect bcl2fastq undetermined
1 parent 2ff8128 commit e15c999

5 files changed

Lines changed: 141 additions & 32 deletions

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‎subworkflows/nf-core/bcl_demultiplex/main.nf‎

Lines changed: 13 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,7 @@ workflow BCL_DEMULTIPLEX {
2020
ch_interop = channel.empty()
2121
ch_logs = channel.empty()
2222
ch_sav_files = channel.empty()
23+
ch_undetermined = channel.empty()
2324

2425
// MODULE: bclconvert
2526
// Demultiplex the bcl files
@@ -28,6 +29,7 @@ workflow BCL_DEMULTIPLEX {
2829
ch_interop = ch_interop.mix(BCLCONVERT.out.interop)
2930
ch_reports = ch_reports.mix(BCLCONVERT.out.reports)
3031
ch_logs = ch_logs.mix(BCLCONVERT.out.logs)
32+
ch_undetermined = ch_undetermined.mix(BCLCONVERT.out.undetermined)
3133
ch_sav_files = ch_sav_files.mix(BCLCONVERT.out.reports)
3234
ch_fastq_with_meta = ch_fastq_with_meta.mix(
3335
generateReadgroupBCLCONVERT(
@@ -46,6 +48,7 @@ workflow BCL_DEMULTIPLEX {
4648
ch_interop = ch_interop.mix(BCL2FASTQ.out.interop)
4749
ch_reports = ch_reports.mix(BCL2FASTQ.out.reports)
4850
ch_stats = ch_stats.mix(BCL2FASTQ.out.stats)
51+
ch_undetermined = ch_undetermined.mix(BCL2FASTQ.out.undetermined)
4952
ch_sav_files = ch_sav_files.mix(BCL2FASTQ.out.stats)
5053
ch_fastq_with_meta = ch_fastq_with_meta.mix(
5154
generateReadgroupBCL2FASTQ(
@@ -83,15 +86,16 @@ workflow BCL_DEMULTIPLEX {
8386
}
8487

8588
emit:
86-
fastq = ch_fastq.fastq
87-
empty_fastq = ch_fastq.empty
88-
reports = ch_reports
89-
stats = ch_stats
90-
interop = ch_interop
91-
logs = ch_logs
92-
sav_report = MULTIQCSAV.out.report
93-
sav_data = MULTIQCSAV.out.data
94-
sav_plots = MULTIQCSAV.out.plots
89+
fastq = ch_fastq.fastq
90+
empty_fastq = ch_fastq.empty
91+
reports = ch_reports
92+
stats = ch_stats
93+
interop = ch_interop
94+
logs = ch_logs
95+
undetermined = ch_undetermined
96+
sav_report = MULTIQCSAV.out.report
97+
sav_data = MULTIQCSAV.out.data
98+
sav_plots = MULTIQCSAV.out.plots
9599
}
96100

97101
def generateReadgroupBCLCONVERT(ch_fastq_list_csv, ch_fastq) {

‎subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,7 @@ nextflow_workflow {
4242
assertAll(
4343
{ assert workflow.success },
4444
{ assert snapshot(
45-
sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "sav_report", "sav_data", "sav_plots"]).collectEntries { key, val ->
45+
sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "sav_report", "sav_data", "sav_plots", "undetermined"]).collectEntries { key, val ->
4646
if (key == "interop") {
4747
return [ key, val.collect { meta, files ->
4848
[
@@ -93,7 +93,7 @@ nextflow_workflow {
9393
assertAll(
9494
{ assert workflow.success },
9595
{ assert snapshot(
96-
sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "sav_report", "sav_data", "sav_plots"]).collectEntries { key, val ->
96+
sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "sav_report", "sav_data", "sav_plots", "undetermined"]).collectEntries { key, val ->
9797
if (key == "fastq")
9898
if (key == "interop") {
9999
return [ key, val.collect { meta, files ->

‎subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap‎

Lines changed: 18 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -170,14 +170,23 @@
170170
],
171171
"stats": [
172172

173+
],
174+
"undetermined": [
175+
[
176+
{
177+
"id": "HMTFYDRXX",
178+
"lane": 1
179+
},
180+
"Undetermined_S0_L001_R1_001.fastq.gz"
181+
]
173182
]
174183
}
175184
],
185+
"timestamp": "2026-03-16T13:47:40.083238326",
176186
"meta": {
177-
"nf-test": "0.9.3",
187+
"nf-test": "0.9.4",
178188
"nextflow": "25.10.4"
179-
},
180-
"timestamp": "2026-03-04T19:55:51.054792"
189+
}
181190
},
182191
"bcl2fastq": {
183192
"content": [
@@ -309,13 +318,16 @@
309318
"Stats.json:md5,8e5f038b8aa9e465599d3575f930e604"
310319
]
311320
]
321+
],
322+
"undetermined": [
323+
312324
]
313325
}
314326
],
327+
"timestamp": "2026-03-16T13:48:09.325036018",
315328
"meta": {
316-
"nf-test": "0.9.3",
329+
"nf-test": "0.9.4",
317330
"nextflow": "25.10.4"
318-
},
319-
"timestamp": "2026-03-04T19:42:28.852443"
331+
}
320332
}
321333
}

‎subworkflows/nf-core/fastq_contam_seqtk_kraken/main.nf‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -39,5 +39,6 @@ workflow FASTQ_CONTAM_SEQTK_KRAKEN {
3939
ch_reports = ch_reports.mix(KRAKEN2.out.report)
4040

4141
emit:
42-
reports = ch_reports // channel: [ [meta], log ]
42+
reports = ch_reports // channel: [ [meta], log ]
43+
reads = SEQTK_SAMPLE.out.reads // channel: [ [meta], reads ]
4344
}

‎subworkflows/nf-core/fastq_contam_seqtk_kraken/tests/main.nf.test.snap‎

Lines changed: 106 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,42 @@
2020
"test.25000.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
2121
]
2222
],
23+
"1": [
24+
[
25+
{
26+
"id": "test",
27+
"single_end": true,
28+
"n_reads": 12500
29+
},
30+
"test.12500_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
31+
],
32+
[
33+
{
34+
"id": "test",
35+
"single_end": true,
36+
"n_reads": 25000
37+
},
38+
"test.25000_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
39+
]
40+
],
41+
"reads": [
42+
[
43+
{
44+
"id": "test",
45+
"single_end": true,
46+
"n_reads": 12500
47+
},
48+
"test.12500_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
49+
],
50+
[
51+
{
52+
"id": "test",
53+
"single_end": true,
54+
"n_reads": 25000
55+
},
56+
"test.25000_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
57+
]
58+
],
2359
"reports": [
2460
[
2561
{
@@ -40,11 +76,11 @@
4076
]
4177
}
4278
],
79+
"timestamp": "2026-03-16T13:43:30.024469728",
4380
"meta": {
44-
"nf-test": "0.9.2",
45-
"nextflow": "25.10.2"
46-
},
47-
"timestamp": "2026-01-15T17:23:21.150863294"
81+
"nf-test": "0.9.4",
82+
"nextflow": "25.10.4"
83+
}
4884
},
4985
"sarscov2 - fastq - [12500, 25000] - krakendb -- stub": {
5086
"content": [
@@ -67,6 +103,42 @@
67103
"test.25000.kraken2.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
68104
]
69105
],
106+
"1": [
107+
[
108+
{
109+
"id": "test",
110+
"single_end": true,
111+
"n_reads": 12500
112+
},
113+
"test.12500.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
114+
],
115+
[
116+
{
117+
"id": "test",
118+
"single_end": true,
119+
"n_reads": 25000
120+
},
121+
"test.25000.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
122+
]
123+
],
124+
"reads": [
125+
[
126+
{
127+
"id": "test",
128+
"single_end": true,
129+
"n_reads": 12500
130+
},
131+
"test.12500.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
132+
],
133+
[
134+
{
135+
"id": "test",
136+
"single_end": true,
137+
"n_reads": 25000
138+
},
139+
"test.25000.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
140+
]
141+
],
70142
"reports": [
71143
[
72144
{
@@ -87,14 +159,14 @@
87159
]
88160
},
89161
[
90-
162+
91163
]
92164
],
165+
"timestamp": "2026-03-16T13:43:39.839595283",
93166
"meta": {
94-
"nf-test": "0.9.2",
95-
"nextflow": "25.10.2"
96-
},
97-
"timestamp": "2026-01-15T17:23:31.030729105"
167+
"nf-test": "0.9.4",
168+
"nextflow": "25.10.4"
169+
}
98170
},
99171
"sarscov2 - fastq - 25000 - krakendb": {
100172
"content": [
@@ -109,6 +181,26 @@
109181
"test.25000.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
110182
]
111183
],
184+
"1": [
185+
[
186+
{
187+
"id": "test",
188+
"single_end": true,
189+
"n_reads": 25000
190+
},
191+
"test.25000_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
192+
]
193+
],
194+
"reads": [
195+
[
196+
{
197+
"id": "test",
198+
"single_end": true,
199+
"n_reads": 25000
200+
},
201+
"test.25000_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
202+
]
203+
],
112204
"reports": [
113205
[
114206
{
@@ -121,10 +213,10 @@
121213
]
122214
}
123215
],
216+
"timestamp": "2026-03-16T13:43:20.617712027",
124217
"meta": {
125-
"nf-test": "0.9.2",
126-
"nextflow": "25.10.2"
127-
},
128-
"timestamp": "2026-01-15T17:23:10.743490624"
218+
"nf-test": "0.9.4",
219+
"nextflow": "25.10.4"
220+
}
129221
}
130-
}
222+
}

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