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Updated samshee #240

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merged 11 commits into from
Aug 12, 2024
+50 −125
Merged

Updated samshee #240

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41a3481
Updated samshee
nschcolnicov Aug 12, 2024
79f0bba
Update conf/modules.config
nschcolnicov Aug 12, 2024
92e7dd0
Updated snap for CI
nschcolnicov Aug 12, 2024
89dc4ee
Merge branch 'samshee_improvements' of https://github.com/nf-core/dem…
nschcolnicov Aug 12, 2024
0df2f24
Update conf/modules.config
apeltzer Aug 12, 2024
f92dfec
Update skip_tools.nf.test.snap
apeltzer Aug 12, 2024
9bb0b6b
Bumped tests to nf-test 0.9.0 everywhere
apeltzer Aug 12, 2024
9441ff0
Merge branch 'dev' of https://github.com/nf-core/demultiplex into sam…
nschcolnicov Aug 12, 2024
62f9850
Merge branch 'samshee_improvements' of https://github.com/nf-core/dem…
apeltzer Aug 12, 2024
8fb01a8
Update version of skip nftest
nschcolnicov Aug 12, 2024
ec12969
Updated nftest version
nschcolnicov Aug 12, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#216](https://github.com/nf-core/demultiplex/pull/216) List fastq reports for R1 and R2 separately in multiqc report.
- [#219](https://github.com/nf-core/demultiplex/pull/219) Modified workflow to store samplesheet in results folder.
- [#217](https://github.com/nf-core/demultiplex/pull/217) Update all nf-core modules and tests.
- [#240](https://github.com/nf-core/demultiplex/pull/240) Updated samshee, stub script and error strategy

### `Fixed`

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4 changes: 4 additions & 0 deletions conf/modules.config
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Expand Up @@ -232,6 +232,10 @@ process {
mode: params.publish_dir_mode
]
}
//Samshee should fail the entire pipeline immediately as it validated the illumina samplesheet to be valid before the pipeline runs. As such, it should not be running more than once & if it fails should stop the pipeline
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withName: SAMSHEE {
errorStrategy = "terminate"
}

}

80 changes: 0 additions & 80 deletions modules/local/samshee/main.nf
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Expand Up @@ -45,90 +45,10 @@ process SAMSHEE {

stub:
"""
#Generate minimal samplesheet
cat <<-END_SAMPLE_SHEET > minimal_samplesheet.csv
[Header]
FileFormatVersion,2
RunName,Run_001
Instrument Type,NextSeq 1000
InstrumentPlatform,NextSeq 1000

[Reads]
Read1Cycles,150
Read2Cycles,150
Index1Cycles,8
Index2Cycles,8

[Settings]

[Data]
Sample_ID,Sample_Name,Description,Sample_Project
Sample1,Sample1,,
END_SAMPLE_SHEET


#Generate minimal schema validator file
cat <<-END_SCHEMA > minimal_schema.json
{
"type": "object",
"properties": {
"Header": {
"type": "object",
"properties": {
"FileFormatVersion": { "type": "integer" },
"RunName": { "type": "string" },
"Instrument Type": { "type": "string" },
"InstrumentPlatform": { "type": "string" }
},
"required": ["FileFormatVersion", "RunName", "Instrument Type", "InstrumentPlatform"]
},
"Reads": {
"type": "object",
"properties": {
"Read1Cycles": { "type": "integer" },
"Read2Cycles": { "type": "integer" },
"Index1Cycles": { "type": "integer" },
"Index2Cycles": { "type": "integer" }
},
"required": ["Read1Cycles", "Read2Cycles", "Index1Cycles", "Index2Cycles"]
},
"Settings": {
"type": "object"
},
"Data": {
"type": "array",
"items": {
"type": "object",
"properties": {
"Sample_ID": { "type": "string" },
"Sample_Name": { "type": "string" },
"Description": { "type": "string" },
"Sample_Project": { "type": "string" }
},
"required": ["Sample_ID", "Sample_Name", "Description", "Sample_Project"]
}
}
},
"required": ["Header", "Reads", "Settings", "Data"]
}
END_SCHEMA

# Run validation command and capture output
output=\$(validate_samplesheet.py minimal_samplesheet.csv minimal_schema.json 2>&1)
status=\$?
# Check if validation failed
if echo "\$output" | grep -q "Validation failed:"; then
echo "\$output" # Print output for debugging
exit 1 # Fail the process if validation failed
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
samshee: \$( python -m pip show --version samshee | grep "Version" | sed -e "s/Version: //g" )
python: \$( python --version | sed -e "s/Python //g" )
END_VERSIONS

# If no validation errors, process exits with status 0
exit \$status
"""
}
50 changes: 25 additions & 25 deletions tests/pipeline/skip_tools.nf.test.snap
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Expand Up @@ -5,9 +5,9 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
"nextflow": "24.04.4"
},
"timestamp": "2024-07-25T20:38:35.033660203"
"timestamp": "2024-08-12T17:10:00.298491082"
},
"skip_fastqc": {
"content": [
Expand All @@ -30,10 +30,10 @@
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "23.10.1"
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-07T15:11:46.12688"
"timestamp": "2024-08-12T17:13:45.68600951"
},
"skip_fastp": {
"content": [
Expand All @@ -56,10 +56,10 @@
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "23.10.1"
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-07T15:09:48.227109"
"timestamp": "2024-08-12T17:11:10.977146544"
},
"skip_multiqc": {
"content": [
Expand All @@ -82,10 +82,10 @@
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "23.10.1"
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-07T15:14:47.991287"
"timestamp": "2024-08-12T17:16:50.422490047"
},
"skip_fastp_fastqc": {
"content": [
Expand All @@ -108,50 +108,50 @@
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "23.10.1"
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-07T15:13:01.794999"
"timestamp": "2024-08-12T17:15:14.973440084"
},
"software_versions_skip_fastqc": {
"content": [
"{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
"nextflow": "24.04.4"
},
"timestamp": "2024-07-25T20:40:12.591107775"
"timestamp": "2024-08-12T17:13:40.000621044"
},
"software_versions_skip_fastp_fastqc": {
"content": [
"{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
"nextflow": "24.04.4"
},
"timestamp": "2024-07-25T20:40:52.373539308"
"timestamp": "2024-08-12T17:15:06.589630757"
},
"software_versions_skip_multiqc": {
"content": [
"{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
"nextflow": "24.04.4"
},
"timestamp": "2024-07-25T20:41:53.704450617"
"timestamp": "2024-08-12T17:16:39.766616774"
},
"software_versions_skip_fastp": {
"content": [
"{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0dev}}"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
"nextflow": "24.04.4"
},
"timestamp": "2024-07-25T20:39:04.450501154"
"timestamp": "2024-08-12T17:11:08.013153743"
},
"skip_trimming": {
"content": [
Expand All @@ -174,9 +174,9 @@
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "23.10.1"
"nf-test": "0.8.4",
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"nextflow": "24.04.4"
},
"timestamp": "2024-08-07T15:08:34.10467"
"timestamp": "2024-08-12T17:10:00.32545302"
}
}
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