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liulab-dfci / RIMA_pipeline

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'NoneType' object is not iterable #13

Open beijish opened 2 years ago

beijish commented 2 years ago

Good afternoon, thank you very much for making the tool available. I have installed RIMA following the GitHub tutorial (AWS), I have the following error when trying to run

snakemake -s RIMA.snakefile -np

InputFunctionException in line 129 of /mnt/panfs1/scratch/wsspaces/svalpione-tide-0/RIMA/RIMA_pipeline/RIMA.snakefile: Error: TypeError: 'NoneType' object is not iterable Wildcards:

Traceback: File "/xxx/RIMA/RIMA_pipeline/RIMA.snakefile", line 99, in all_targets File "/xxx/RIMA/RIMA_pipeline/./modules/preprocess/preprocess_individual.snakefile", line 30, in preprocess_individual_targets

Any help please? Thank you in advance

SV

beijish commented 2 years ago

Good afternoon,

I think the problem might come from the fact that I have single end FASTQ files as input files. Does the pipeline support single end inputs? If yes, how can I modify the config.yaml so that It can run? Thank you

SV