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sateeshperisateeshperi
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update test names and bwameth index md5
1 parent c856ff9 commit fd2419e

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+68
-89
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2 files changed

+68
-89
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‎subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test

Lines changed: 10 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -46,17 +46,14 @@ nextflow_workflow {
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test("Params: bismark | generate bismark index (bowtie2)") {
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when {
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params {
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aligner = "bismark"
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}
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workflow {
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"""
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input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
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input[1] = [] // fasta_index
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input[2] = [] // bismark_index
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input[3] = [] // bwameth_index
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input[4] = "bismark" // aligner
59-
input[5] = false // run_picard_collecthsmetrics
56+
input[5] = false // collecthsmetrics
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"""
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}
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}
@@ -78,17 +75,14 @@ nextflow_workflow {
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test("Params: bismark_hisat | download bismark index (hisat2)") {
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when {
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params {
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aligner = "bismark_hisat"
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}
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workflow {
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"""
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input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
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input[1] = [] // fasta_index
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input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true)
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input[3] = [] // bwameth_index
9084
input[4] = "bismark_hisat" // aligner
91-
input[5] = false // run_picard_collecthsmetrics
85+
input[5] = false // collecthsmetrics
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"""
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}
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}
@@ -110,17 +104,14 @@ nextflow_workflow {
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test("Params: bismark_hisat | generate bismark index (hisat2)") {
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when {
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params {
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aligner = "bismark_hisat"
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}
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workflow {
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"""
118109
input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
119110
input[1] = [] // fasta_index
120111
input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true)
121112
input[3] = [] // bwameth_index
122113
input[4] = "bismark_hisat" // aligner
123-
input[5] = false // run_picard_collecthsmetrics
114+
input[5] = false // collecthsmetrics
124115
"""
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}
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}
@@ -139,21 +130,17 @@ nextflow_workflow {
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}
140131
}
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142-
test("Params: bismark | download bismark index (bowtie2) | run_picard_collecthsmetrics") {
133+
test("Params: bismark | download bismark index (bowtie2) | collecthsmetrics") {
143134

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when {
145-
params {
146-
aligner = "bismark"
147-
run_picard_collecthsmetrics = true
148-
}
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workflow {
150137
"""
151138
input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
152139
input[1] = [] // fasta_index
153140
input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz', checkIfExists: true)
154141
input[3] = [] // bwameth_index
155142
input[4] = "bismark" // aligner
156-
input[5] = true // run_picard_collecthsmetrics
143+
input[5] = true // collecthsmetrics
157144
"""
158145
}
159146
}
@@ -175,17 +162,14 @@ nextflow_workflow {
175162
test("Params: bwameth | download fasta index | download bwameth index") {
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177164
when {
178-
params {
179-
aligner = "bwameth"
180-
}
181165
workflow {
182166
"""
183167
input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
184168
input[1] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true)
185169
input[2] = [] // bismark index
186170
input[3] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true)
187171
input[4] = "bwameth" // aligner
188-
input[5] = false // run_picard_collecthsmetrics
172+
input[5] = false // collecthsmetrics
189173
"""
190174
}
191175
}
@@ -207,17 +191,14 @@ nextflow_workflow {
207191
test("Params: bwameth | generate fasta index | download bwameth index") {
208192

209193
when {
210-
params {
211-
aligner = "bwameth"
212-
}
213194
workflow {
214195
"""
215196
input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
216197
input[1] = [] //fasta index
217198
input[2] = [] // bismark index
218199
input[3] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true)
219200
input[4] = "bwameth" // aligner
220-
input[5] = false // run_picard_collecthsmetrics
201+
input[5] = false // collecthsmetrics
221202
"""
222203
}
223204
}
@@ -239,17 +220,14 @@ nextflow_workflow {
239220
test("Params: bwameth | generate fasta index | generate bwameth index") {
240221

241222
when {
242-
params {
243-
aligner = "bwameth"
244-
}
245223
workflow {
246224
"""
247225
input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
248226
input[1] = [] // fasta_index
249227
input[2] = [] // bismark index
250228
input[3] = [] // bwameth index
251229
input[4] = "bwameth" // aligner
252-
input[5] = false // run_picard_collecthsmetrics
230+
input[5] = false // collecthsmetrics
253231
"""
254232
}
255233
}
@@ -268,21 +246,17 @@ nextflow_workflow {
268246
}
269247
}
270248

271-
test("Params: bwameth | generate fasta index | download bwameth index | run_picard_collecthsmetrics") {
249+
test("Params: bwameth | generate fasta index | download bwameth index | collecthsmetrics") {
272250

273251
when {
274-
params {
275-
aligner = "bwameth"
276-
run_picard_collecthsmetrics = true
277-
}
278252
workflow {
279253
"""
280254
input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
281255
input[1] = [] //fasta index
282256
input[2] = [] // bismark index
283257
input[3] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true)
284258
input[4] = "bwameth" // aligner
285-
input[5] = true // run_picard_collecthsmetrics
259+
input[5] = true // collecthsmetrics
286260
"""
287261
}
288262
}

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

Lines changed: 58 additions & 53 deletions
Original file line numberDiff line numberDiff line change
@@ -214,6 +214,55 @@
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},
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"timestamp": "2024-12-13T18:04:54.292757645"
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},
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"Params: bwameth | generate fasta index | download bwameth index | collecthsmetrics": {
218+
"content": [
219+
[
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[
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{
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},
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"genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
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]
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],
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[
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[
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{
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},
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"genome.fa.fai:md5,84f5b44c25877ac58b154706cc8bc451"
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]
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],
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[
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],
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[
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[
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{
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},
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[
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"genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
245+
"genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b",
246+
"genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3",
247+
"genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110",
248+
"genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e",
249+
"genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66",
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"genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d"
251+
]
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]
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],
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[
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"versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1",
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"versions.yml:md5,dfb3bc1adbc94d00aec14dad16eee3df",
257+
"versions.yml:md5,ee0146f5d2942f9ff466bf275567515e"
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]
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],
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"meta": {
261+
"nf-test": "0.9.2",
262+
"nextflow": "24.10.4"
263+
},
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"timestamp": "2025-04-15T11:09:44.719682704"
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},
217266
"Params: bismark_hisat | download bismark index (hisat2)": {
218267
"content": [
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[
@@ -286,7 +335,12 @@
286335
]
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],
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[
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"/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai"
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[
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{
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},
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"/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai"
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]
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],
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[
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@@ -313,12 +367,12 @@
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]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nf-test": "0.9.0",
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"nextflow": "24.10.2"
318372
},
319-
"timestamp": "2024-12-13T18:05:04.769597102"
373+
"timestamp": "2025-06-11T20:45:19.092285"
320374
},
321-
"Params: bismark | download bismark index (bowtie2) | run_picard_collecthsmetrics": {
375+
"Params: bismark | download bismark index (bowtie2) | collecthsmetrics": {
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"content": [
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[
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[
@@ -437,54 +491,5 @@
437491
"nextflow": "24.10.2"
438492
},
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"timestamp": "2024-12-13T18:04:34.428155309"
440-
},
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"Params: bwameth | generate fasta index | download bwameth index | run_picard_collecthsmetrics": {
442-
"content": [
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[
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[
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{
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},
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"genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
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]
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],
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[
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[
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{
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},
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"genome.fa.fai:md5,84f5b44c25877ac58b154706cc8bc451"
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]
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],
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[
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],
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[
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[
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{
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},
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[
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"genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
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"genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b",
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"genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3",
471-
"genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110",
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"genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e",
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"genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66",
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"genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d"
475-
]
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]
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],
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[
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"versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1",
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"versions.yml:md5,dfb3bc1adbc94d00aec14dad16eee3df",
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"versions.yml:md5,ee0146f5d2942f9ff466bf275567515e"
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]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.4"
487-
},
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"timestamp": "2025-04-15T11:09:44.719682704"
489494
}
490495
}

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