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a-h-b / dadasnake

Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
GNU General Public License v3.0
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Setup and cutadapt cyclic dependency issue #12

Closed Fred-White94 closed 3 years ago

Fred-White94 commented 3 years ago

Hi - sorry for multiple questions but I really want to use this pipeline!

  1. I set up (installed the pipeline as per the readme but when trying to run (on a slurm system using -c) I get the message: " The person who set up dadasnake disabled changing resource settings." and the pipeline then only claims one core. How can I re enable the resource setting change?

  2. When trying a dryrun I get an error from the cutadapt.smk rule combine_or_rename "CyclicGraphException in line 22 of /dadasnake/workflow/rules/cutadapt.smk: Cyclic dependency on rule combine_or_rename."

    It is not so clear why this error is occurring - could it be to do with the samples.tsv file?

    Thanks again for your time!

Fred-White94 commented 3 years ago

Answers to my own questions come directly from the readme.

  1. change the value of LOCK_SETTINGS in VARIABLE_CONFIG file
  2. Ensure that in samples.tsv file the library column is not the same values as the sample column