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Update bases2fastq (#9253)
* Update bases2fastq * Update to most recent version
1 parent 96b96cd commit 01bfb37

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4 files changed

+48
-34
lines changed

4 files changed

+48
-34
lines changed

‎modules/nf-core/bases2fastq/main.nf‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2,15 +2,16 @@ process BASES2FASTQ {
22
tag "$meta.id"
33
label 'process_high'
44

5-
container "docker.io/elembio/bases2fastq:1.8.0"
5+
container "docker.io/elembio/bases2fastq:2.3.0"
66

77
input:
88
tuple val(meta), path(run_manifest), path(run_dir)
99

1010
output:
1111
tuple val(meta), path('output/Samples/**/*_R*.fastq.gz'), emit: sample_fastq
1212
tuple val(meta), path('output/Samples/**/*_stats.json') , emit: sample_json
13-
tuple val(meta), path('output/*.html') , emit: qc_report
13+
tuple val(meta), path('output/*_QC.html') , emit: qc_report
14+
tuple val(meta), path('output/multiqc_report.html') , emit: multiqc_report, optional: true
1415
tuple val(meta), path('output/RunStats.json') , emit: run_stats
1516
tuple val(meta), path('output/RunManifest.json') , emit: generated_run_manifest
1617
tuple val(meta), path('output/Metrics.csv') , emit: metrics
@@ -26,7 +27,6 @@ process BASES2FASTQ {
2627
error "BASES2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
2728
}
2829
def args = task.ext.args ?: ''
29-
def prefix = task.ext.prefix ?: "${meta.id}"
3030
def runManifest = run_manifest ? "-r ${run_manifest}" : ""
3131
"""
3232
bases2fastq \\
@@ -54,6 +54,7 @@ process BASES2FASTQ {
5454
echo | gzip > output/Samples/DefaultSample/DefaultSample_R1.fastq.gz
5555
echo | gzip > output/Samples/DefaultSample/DefaultSample_R2.fastq.gz
5656
touch output/Bases2Fastq-Sim_QC.html
57+
touch output/multiqc_report.html
5758
touch output/RunStats.json
5859
touch output/Samples/DefaultSample/DefaultSample_stats.json
5960
touch versions.yml

‎modules/nf-core/bases2fastq/meta.yml‎

Lines changed: 13 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -59,10 +59,21 @@ output:
5959
description: |
6060
Groovy Map containing sample information
6161
e.g. [ id:'test', single_end:false ]
62-
- output/*.html:
62+
- output/*_QC.html:
6363
type: file
6464
description: QC HTML report
65-
pattern: "output/*.html"
65+
pattern: "output//*_QC.html"
66+
ontologies: []
67+
multiqc_report:
68+
- - meta:
69+
type: map
70+
description: |
71+
Groovy Map containing sample information
72+
e.g. [ id:'test', single_end:false ]
73+
- output/multiqc_report.html:
74+
type: file
75+
description: Multiqc HTML report
76+
pattern: "output/multiqc_report.html"
6677
ontologies: []
6778
run_stats:
6879
- - meta:

‎modules/nf-core/bases2fastq/tests/main.nf.test‎

Lines changed: 15 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -11,10 +11,13 @@ nextflow_process {
1111

1212
setup {
1313
run("UNTAR") {
14-
script "modules/nf-core/untar/main.nf"
14+
script "../../untar/main.nf"
1515
process {
1616
"""
17-
input[0] = Channel.of([ [id: "sim-data", samplesheet: file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv", checkIfExists: true)], file("https://github.com/nf-core/test-datasets/raw/demultiplex/testdata/sim-data/sim-data.tar.gz", checkIfExists: true) ])
17+
input[0] = [
18+
[id:'sim-data'],
19+
file("https://github.com/nf-core/test-datasets/raw/demultiplex/testdata/sim-data/sim-data.tar.gz", checkIfExists:true)
20+
]
1821
"""
1922
}
2023
}
@@ -24,8 +27,10 @@ nextflow_process {
2427
when {
2528
process {
2629
"""
27-
input[0]= UNTAR.out.untar.map{meta, untar -> [meta, meta.samplesheet, untar]}
28-
30+
input[0] = Channel.of([
31+
[id:'sim-data'],
32+
file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv", checkIfExists:true)
33+
]).join(UNTAR.out.untar)
2934
"""
3035
}
3136
}
@@ -40,6 +45,7 @@ nextflow_process {
4045
process.out.sample_fastq,
4146
process.out.versions,
4247
file(process.out.qc_report[0][1]).name,
48+
file(process.out.multiqc_report[0][1]).name,
4349
file(process.out.run_stats[0][1]).name,
4450
file(process.out.sample_json[0][1]).name,
4551
).match()
@@ -54,8 +60,11 @@ nextflow_process {
5460
when {
5561
process {
5662
"""
57-
input[0]= UNTAR.out.untar.map{meta, untar -> [meta, meta.samplesheet, untar]}
58-
63+
input[0]= [
64+
[id: "sim-data"],
65+
[],
66+
[]
67+
]
5968
"""
6069
}
6170
}

‎modules/nf-core/bases2fastq/tests/main.nf.test.snap‎

Lines changed: 16 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -4,35 +4,31 @@
44
[
55
[
66
{
7-
"id": "sim-data",
8-
"samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
7+
"id": "sim-data"
98
},
109
"Metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
1110
]
1211
],
1312
[
1413
[
1514
{
16-
"id": "sim-data",
17-
"samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
15+
"id": "sim-data"
1816
},
1917
"RunManifest.json:md5,d41d8cd98f00b204e9800998ecf8427e"
2018
]
2119
],
2220
[
2321
[
2422
{
25-
"id": "sim-data",
26-
"samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
23+
"id": "sim-data"
2724
},
2825
"UnassignedSequences.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
2926
]
3027
],
3128
[
3229
[
3330
{
34-
"id": "sim-data",
35-
"samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
31+
"id": "sim-data"
3632
},
3733
[
3834
"DefaultSample_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
@@ -48,45 +44,41 @@
4844
"DefaultSample_stats.json"
4945
],
5046
"meta": {
51-
"nf-test": "0.8.4",
52-
"nextflow": "24.04.2"
47+
"nf-test": "0.9.2",
48+
"nextflow": "25.04.6"
5349
},
54-
"timestamp": "2024-06-08T13:22:53.536627298"
50+
"timestamp": "2025-10-27T14:56:40.499735343"
5551
},
5652
"sim-data.tar.gz - bcl": {
5753
"content": [
5854
[
5955
[
6056
{
61-
"id": "sim-data",
62-
"samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
57+
"id": "sim-data"
6358
},
6459
"Metrics.csv:md5,1db1769b9b5917b8353e05bf8fd699c7"
6560
]
6661
],
6762
[
6863
[
6964
{
70-
"id": "sim-data",
71-
"samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
65+
"id": "sim-data"
7266
},
7367
"RunManifest.json:md5,d584cdf00f577937a6cb691bb5331fe8"
7468
]
7569
],
7670
[
7771
[
7872
{
79-
"id": "sim-data",
80-
"samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
73+
"id": "sim-data"
8174
},
8275
"UnassignedSequences.csv:md5,11c1693830ce941b8cfb8d2431a59097"
8376
]
8477
],
8578
[
8679
[
8780
{
88-
"id": "sim-data",
89-
"samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
81+
"id": "sim-data"
9082
},
9183
[
9284
"DefaultSample_R1.fastq.gz:md5,44ff0899ad4568a5cab7ccb7df9928e8",
@@ -95,16 +87,17 @@
9587
]
9688
],
9789
[
98-
"versions.yml:md5,018cd865ddeaf6d03a2cabf6da664ec8"
90+
"versions.yml:md5,757e8e083d5804e0ef04d5ee4fd03a3f"
9991
],
10092
"20230404-Bases2Fastq-Sim_QC.html",
93+
"multiqc_report.html",
10194
"RunStats.json",
10295
"DefaultSample_stats.json"
10396
],
10497
"meta": {
105-
"nf-test": "0.8.4",
106-
"nextflow": "24.04.2"
98+
"nf-test": "0.9.2",
99+
"nextflow": "25.04.6"
107100
},
108-
"timestamp": "2024-06-08T13:22:38.54589349"
101+
"timestamp": "2025-10-27T15:17:21.580320078"
109102
}
110103
}

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