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Genomics
Quality control,before anything else
FastQC across every read file you point it at.One HTML report per input, written back to output.
FastQC 0.12.14 cores · 4 GBRuns as a job
hub://fastqc
$ dxflow workflow create --identity fastqc hub://fastqc
$ dxflow workflow start fastqc --override env.job.THREADS=8
01Pick a machinecores, memory and a rate per hour
02Create the workflowpulled from the hub, once
03Run it, then stopstopped when the work is done
The application
A report,for every file
FASTQ, BAM or SAM in; an HTML report and a ZIP back out.
Any of three formats
FASTQ, BAM or SAM, matched by the INPUT glob you set at the start.
A report each
An HTML report and a ZIP of the numbers, one pair for every input.
Files in parallel
THREADS is how many files it takes at once, not threads in a file.
The job
It runs,and then it stops
A job, not a session — it ends when the last report is written.
inputInputyour reads, mounted read-only
outputOutputthe reports land here
Point INPUT at themThe default glob is /data/input/*.fastq.gz — override it.
Watch it from the CLIdxflow workflow logs follows the run, and list shows the state.
Run FastQC on your own machinePick a machine that meets it, and it opens about a minute after you ask.