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Regex for paired sequencing in pipeline_readqc #75

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IanSudbery opened this issue Oct 22, 2018 · 0 comments
Open

Regex for paired sequencing in pipeline_readqc #75

IanSudbery opened this issue Oct 22, 2018 · 0 comments

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@IanSudbery
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For paired reads in pipeline_readQC, the input regex is:

r"(?P<track>[^/]+).(?P<suffix>fastq.1.gz|fastq.gz|sra|csfasta.gz|remote)"```

The output of the fastqc task is recorded as
```
"fastqc.dir/{track[0}.fastqc"
```

This would mean that `Tissue-condition-replicate.fastq.1.gz` and `Tissue-condition-replicate.fastq.2.gz` but mapped onto `Tissue-condition-replicate.fastqc`. But in actaul fact the fastqc processor outputs `Tissue-condition_fastq_1.fastqc` and `Tissue-conditions-replicate_fastq_2.fastqc`.

This is mostly harmless other than the fastqc will always be rerun. However it does mean that if `autoremove=1`, the pipeline won't run, as it is looking for `Tissue-conditions-replicate.fastqc`.
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