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Full Test Data #580

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Jun 21, 2022
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Full Test Data #580

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bf5ddca
update the test_full samplesheet to be full open source WXS data from…
Jun 8, 2022
84e3b04
Update conf/test_full.config
nickhsmith Jun 8, 2022
3125a1e
Update conf/test_full.config
nickhsmith Jun 8, 2022
370f1cc
Update conf/test_full.config
nickhsmith Jun 8, 2022
7543400
update CHANGELOG
Jun 8, 2022
b591db8
update CHANGELOG
Jun 8, 2022
6f0a0a7
Update CHANGELOG.md
nickhsmith Jun 8, 2022
c1a8c7a
Update tests/csv/3.0/test_full_data.csv
ggabernet Jun 21, 2022
91ed426
Update tests/csv/3.0/test_full_data.csv
ggabernet Jun 21, 2022
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2 changes: 2 additions & 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

### Changed

- [#580](https://github.com/nf-core/sarek/pull/580) - changed the test_full config to real public WXS data. 1 sample WXS germline, 1 Tumor/Normal pair. https://doi.org/10.1038/sdata.2016.25 and https://doi.org/10.1038/s41587-021-00994-5
- [#383](https://github.com/nf-core/sarek/pull/383), [#528](https://github.com/nf-core/sarek/pull/528) - Update `CHANGELOG`
- [#390](https://github.com/nf-core/sarek/pull/390) - Update `nextflow_schema.json`
- [#408](https://github.com/nf-core/sarek/pull/408) - Sync `TEMPLATE` with `tools` `2.0.1`
Expand Down Expand Up @@ -899,3 +900,4 @@ First release under the `Sarek` name, from the National Park in Northern Sweden
## [0.8](https://github.com/SciLifeLab/Sarek/releases/tag/0.8) - 2016-11-16

## [0.1] - 2016-04-05

10 changes: 3 additions & 7 deletions conf/test_full.config
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Expand Up @@ -15,14 +15,10 @@ params {
config_profile_description = 'Full test dataset to check pipeline function'

// Input data for full size test
// TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
// TODO nf-core: Give any required params for the test so that command line flags are not needed
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
input = "${baseDir}/tests/csv/3.0/test_full_data.csv"
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// Input data for full size test
// TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
// TODO nf-core: Give any required params for the test so that command line flags are not needed
wes = true

// Ignore `--input` as otherwise the parameter validation will throw an error
schema_ignore_params = 'genomes,input,modules'
schema_ignore_params = 'genomes'
}
4 changes: 4 additions & 0 deletions tests/csv/3.0/test_full_data.csv
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@@ -0,0 +1,4 @@
patient,status,sample,lane,fastq_1,fastq_2
HG002,0,HG002,1,s3://giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_Illumina_2x250bps/reads/D1_S1_L001_R1_001.fastq.gz,s3://giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_Illumina_2x250bps/reads/D1_S1_L001_R2_001.fastq.gz
HCC1395,0,HCC1395-Normal,1,https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR789/001/SRR7890851/SRR7890851_1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR789/001/SRR7890851/SRR7890851_2.fastq.gz
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I would recommend to upload those directly into our S3 bucket to avoid issues that occur when the file download on S3 times out

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I can do that if you like, let me know @FriederikeHanssen

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should we just test it out with the first sample so far?

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HCC1395,1,HCC1395-Tumor,1,https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR789/000/SRR7890850/SRR7890850_1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR789/000/SRR7890850/SRR7890850_2.fastq.gz
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