V - nextseq

M - MiSeq

FS - iSeq

local versions:

LOCALLY:

  1. look at sample sheets and get run name
  2. pull runs from basespace:
    1. username: [email protected]
    2. password: Pathogens@115
    3. sample sheets live here: basespace illumina —> Runs —> find run —> https://basespace.illumina.com/run/277652398/details get the run/*/details, want the * —> runID == 277652398 —> Latest Analyis (FASTQ…) —> view files —> download SampleSheetUsed.csv and download —> rename (SampleSheet_${runID}.csv) and put in working dir on server (see next step) and in local working dir
    4. put renamed sheet on server ahdc01 /local/workdir/GoodmanLab_shared/CARBrunQC
    5. THEN at the end - QC summary goes from server to local

SERVER

  1. now get fastQs from basespace —> step 2 below ./scripts/getRunFastQsCARBonly.awk
  2. make CMDs run (for loop in workflow.sh)
    1. pay attention to cores used 10 or 12 per cmd line.
    2. parallel 3x3
    3. may take some time to complete running!
  3. FINISH

1/ workflow.sh is the file with all the command lines to do per run to go from SampleSheet to NCBI SRA compliant files

workflow.sh