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toil-rnaseq cutadapt error when using local input fastq #405
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@Jeltje — Thanks! I'll get a fix up once I'm up on campus, should only take a few minutes. |
jvivian
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fnothaft
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Pass correct arguments to cutadapt (resolves #405)
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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
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