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Arcadia-Science / 2023-amblyomma-americanum-txome-assembly

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Make metadata and trinity params configurable; minor input fix #16

Closed giladmishne closed 10 months ago

giladmishne commented 10 months ago
  1. Make metadata configurable, so that the pipeline can be run on a different/smaller number of accessions (e.g. for testing).
  2. Fix an issue with fastp rule inputs that caused it to try to read fastqs aggregated by assembly group rather than library name, resulting in: 
    Building DAG of jobs...
MissingInputException in rule fastp in file /Users/giladmishne/dev/2023-amblyomma-americanum-txome-assembly/Snakefile, line 90:
Missing input files for rule fastp:
output: outputs/read_qc/fastp/peaae2cellline.json, outputs/read_qc/fastp/peaae2cellline.html, outputs/read_qc/fastp/peaae2cellline.fq.gz
wildcards: illumina_lib_name=peaae2cellline
affected files:
    outputs/read_qc/raw_combined/peaae2cellline.fq.gz