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toil-rnaseq cutadapt error when using local input fastq #405

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Jeltje opened this issue Aug 9, 2016 · 1 comment
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toil-rnaseq cutadapt error when using local input fastq #405

Jeltje opened this issue Aug 9, 2016 · 1 comment
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@Jeltje
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Jeltje commented Aug 9, 2016

toil-scripts (2.0.5)

Trying to run with local fastq, so the manifest looks like this:
fq paired localin file:///mnt/test_cgl1/testinput/C021_0006_002221_BR_Whole_T2_K1STX_A12445_000_R1.fastq.gz,file:///mnt/test_cgl1/testinput/C021_0006_002221_BR_Whole_T2_K1STX_A12445_000_R2.fastq.gz

I did not change the cutadapt settings in the config file, but I get this error:
TypeError: run_cutadapt() takes exactly 5 arguments (4 given)

full log
config
manifest

@jvivian
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jvivian commented Aug 9, 2016

@Jeltje — Thanks! I'll get a fix up once I'm up on campus, should only take a few minutes.

fnothaft added a commit that referenced this issue Aug 9, 2016
Pass correct arguments to cutadapt (resolves #405)
fnothaft added a commit that referenced this issue Aug 9, 2016
Cherrypick to master (resolves #399, resolves #404, resolves #405)
@jpfeil jpfeil removed the in progress label Aug 9, 2016
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