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318 update for tes compliance #320

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Oct 15, 2024
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3 changes: 3 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [PR #303](https://github.com/nf-core/fetchngs/pull/303) - Update wget container for SRA_FASTQ_FTP from 1.20.1 to 1.21.4
- [PR #305](https://github.com/nf-core/fetchngs/pull/305) - Update module sratools/prefetch for reliable download integrity check
- [PR #316](https://github.com/nf-core/fetchngs/pull/316) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD
- [PR #320](https://github.com/nf-core/fetchngs/pull/320) - Update module multiqc_mappings_config and sratools/prefetch for TES compliance
maxulysse marked this conversation as resolved.
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- [PR #320](https://github.com/nf-core/fetchngs/pull/320) - Refactor workflow tests
- [PR #323](https://github.com/nf-core/fetchngs/pull/323) - Template update for nf-core/tools v3.0.2

### Software dependencies
Expand Down Expand Up @@ -42,6 +44,7 @@ Special thanks to the following for their contributions to the release:
- [Maxime Garcia](https://github.com/maxulysse)
- [Sateesh Peri](https://github.com/sateeshperi)
- [Sebastian Uhrig](https://github.com/suhrig)
- [Venkat Malladi](https://github.com/vsmalladi)

Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

Expand Down
2 changes: 1 addition & 1 deletion modules.json
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
},
"sratools/prefetch": {
"branch": "master",
"git_sha": "1fc29f92e439d5631fdf34b8ac4687297d70f5ec",
"git_sha": "368e6c90b91adbd171e7c0a1c85a700b86a915af",
"installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
},
"untar": {
Expand Down
6 changes: 3 additions & 3 deletions modules/local/aspera_cli/tests/main.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -67,9 +67,9 @@
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-02-28T11:52:00.601018"
"timestamp": "2024-09-17T09:16:31.501413"
}
}
2 changes: 1 addition & 1 deletion modules/local/multiqc_mappings_config/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ process MULTIQC_MAPPINGS_CONFIG {
path csv

output:
path "*yml" , emit: yml
path "*config.yml" , emit: yml
path "versions.yml", emit: versions

script:
Expand Down
16 changes: 5 additions & 11 deletions modules/local/multiqc_mappings_config/tests/main.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,7 @@
"content": [
{
"0": [
[
"multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
"versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
]
"multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a"
],
"1": [
"versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
Expand All @@ -15,17 +12,14 @@
"versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
],
"yml": [
[
"multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
"versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
]
"multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-02-28T11:52:12.65888"
"timestamp": "2024-09-17T09:16:46.557614"
}
}
8 changes: 4 additions & 4 deletions modules/local/sra_fastq_ftp/tests/main.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -67,9 +67,9 @@
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-02-28T11:51:51.301654"
"timestamp": "2024-09-17T09:16:57.715689"
}
}
}
6 changes: 3 additions & 3 deletions modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,9 @@
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-02-28T11:52:05.345153"
"timestamp": "2024-09-17T09:17:11.040523"
}
}
6 changes: 3 additions & 3 deletions modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,9 @@
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-02-28T11:51:45.748227"
"timestamp": "2024-09-17T09:17:23.371547"
}
}

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12 changes: 6 additions & 6 deletions modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap

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2 changes: 0 additions & 2 deletions modules/nf-core/sratools/prefetch/environment.yml

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14 changes: 13 additions & 1 deletion modules/nf-core/sratools/prefetch/main.nf

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1 change: 1 addition & 0 deletions modules/nf-core/sratools/prefetch/meta.yml

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22 changes: 22 additions & 0 deletions modules/nf-core/sratools/prefetch/tests/main.nf.test

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53 changes: 46 additions & 7 deletions modules/nf-core/sratools/prefetch/tests/main.nf.test.snap

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2 changes: 1 addition & 1 deletion nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -248,7 +248,7 @@ validation {
\033[0;35m ${manifest.name} ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x

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33 changes: 11 additions & 22 deletions workflows/sra/tests/main.nf.test
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,9 @@ nextflow_workflow {
test("Parameters: default") {

when {
params {
outdir = "$outputDir"
}
workflow {
"""
input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
Expand All @@ -23,29 +26,15 @@ nextflow_workflow {
}

then {
assert workflow.success

assertAll(
{
with(workflow.out.samplesheet) {
assert path(get(0)).readLines().size() == 4
assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
assert path(get(0)).text.contains('Illumina HiSeq 2500')
}
},
{
with(workflow.out.mappings) {
assert path(get(0)).readLines().size() == 4
assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
assert path(get(0)).text.contains('Illumina HiSeq 2500')
}
},
{
with(workflow.out.sample_mappings) {
assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
}
}
{ assert workflow.success},
{ assert snapshot(
file(workflow.out.samplesheet[0]).name,
workflow.out.mappings,
workflow.out.sample_mappings,
workflow.out.sra_metadata,
workflow.out.versions
).match() }
)
}
}
Expand Down
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