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seqCenter parameter needs to be reconciled #318

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MadraghRua opened this issue Oct 16, 2019 · 1 comment
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seqCenter parameter needs to be reconciled #318

MadraghRua opened this issue Oct 16, 2019 · 1 comment
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@MadraghRua
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I was running the rna-seq pipeline through AWS Batch yesterday as follows: aws batch submit-job --job-name nf-core-rnaseq --job-queue default-35e75ad0-eadc-11e9-b677-0eedb7eead80 --job-definition nextflow --container-overrides command=nf-core/rnaseq,"--reads","'s3://1000genomes/phase3/data/HG00243/sequence_read/SRR*_{1,2}.filt.fastq.gz'","--genome","GRCh37","--skip_qc"

I got through a number of steps until the following warning came up: WARN: Access to undefined parameter seqCenter -- Initialise it to a default value eg. params.seqCenter = some_value

With some investigation from Hpatel the problem appears to be that the parameter name was changed between 1.3 and 1.4. The parameter name should now be changed to seq_center throughout the repository.

@apeltzer apeltzer added this to the 1.4.1 milestone Oct 17, 2019
@drpatelh drpatelh mentioned this issue Oct 17, 2019
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@drpatelh
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Fixed in #319

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