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jpuritz / dDocent

a bash pipeline for RAD sequencing
ddocent.com
MIT License
52 stars 42 forks source link

change trim logging #41

Closed pdimens closed 6 years ago

pdimens commented 6 years ago

changed structure of new logging format of trimming

pdimens commented 6 years ago

With the html/json outputting of fastp, needed to change the format outfiles. I also restructured the order of operations a bit to have cleaner directory structure during the a dDocent run:

make trim reports directory trim_reports (unpaired doesn't exist anymore!) loop: trim move report to directory rinse+repeat

pdimens commented 6 years ago

Also, do you want the correction module for paired-end reads that fastp has? 

-c, --correction                   enable base correction in overlapped regions (only for PE data), default is disabled
      --overlap_len_require          the minimum length of the overlapped region for overlap analysis based adapter trimming and correction. 30 by default. (int [=30])
      --overlap_diff_limit           the maximum difference of the overlapped region for overlap analysis based adapter trimming and correction. 5 by default. (int [=5])
jpuritz commented 6 years ago

I could go either way with the corrections