Full Test Data #580
Full Test Data #580
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
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I will say that these are real life examplse of WXS, but we could down-sample or find sequencing runs with less coverage if the storage/compute time is too large. |
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If you can just update the CHANGELOG that would be perfect. |
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@nickhsmith from what publication is the paired data coming from? |
Good point. I'll add that to the log |
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Wondering if this large file staging will work. Might have to upload htem to the bucket directly and then change the paths |
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
We can move them to whichever bucket we'd like |
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@nf-core-bot fix linting |
tests/csv/3.0/test_full_data.csv
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| 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?
tests/csv/3.0/test_full_data.csv
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| 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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should we just test it out with the first sample so far?
update the test_full samplesheet to be full open source WXS data from GIAB and NCBI