Runing pipeline

[DeaconOfBiology]

• [ ] Run pipeline to:
  • [ ] trim raw reads
  • [ ] download host reference genomes
    • JobID: 11161798
      • This job failed. See first comment below
    • JobID: 11161965
      • This job failed. See second comment below
    • JobID: 11162659

[DeaconOfBiology]

• JobID: 11161798: Apparently this version of snakemake can not take in bash script in the arguement "script:". I got the following error:
  • "Unsupported script: Expecting either Python (.py), R (.R), RMarkdown (.Rmd) or Julia (.jl) script."

I added the script path to "params" and changed the argument "script" to "shell". Going to try again.

[DeaconOfBiology]

• JobID: 11161965 I made a mistake by giving the same output read file for the fr1 and fr2 slot in the in the shell section of the clean_raw_reads rule in the file readQC.smk. Made the required change and running again.