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 --start

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.

How you run it

Point it at the reads,and read what comes back

Files go up into input, reports come down out of output, and three variables sit between them.

INPUTThe glob it reads. FASTQ by default, and it takes BAM or SAM just as well.

THREADSHow many files it works through at once. Set it to 1 and it goes one at a time.

EXTRAAnything else FastQC accepts, handed to it untouched.

a run, end to end

$ dxflow artifact upload sample_R1.fastq.gz input/

$ dxflow workflow start fastqc --override env.job.INPUT=/data/input/*.bam

$ dxflow artifact download output/ ./reports/

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.

Good to know

A pass, a warnor a fail, per module

Every input leaves two files behind, and every module inside them carries a verdict.

The pair it writes

An HTML report to read, and a zip holding the tables behind it. Pass --extract to unpack those too.

What to look at first

Quality falling away at the 3' end means trimming. An odd GC curve usually means something else got in.

What comes after

Adapter content sends you to a trimmer. Reads that came back clean go straight on to alignment.

The image

Pulled once,then it stays

FastQC arrives as one image. This is what comes down the first time, and what the disk should have free for it.

164Mamd64compressed, the way the registry counts it

10GOn diskunpacked, with room to work beside it

ghcr.io/dxflow-ai/fastqc:latestPublished from the hub, pulled on the first start and kept for the ones after it.

amd64 onlyOne architecture is published, so pick a machine that matches it.

What it asks for

What it wants,and what it needs

The definition asks for 4 cores and 4 GB. The image comes up on less than that, and a start given --fit trims the ask to whatever the machine actually has.

4 cores · 4 GBAsks forwhat the definition writes down

2 cores · 2 GBRuns onthe least the image comes up on

Not neededGPUit works on the cores alone

The ask is not the floorThe definition writes down what suits the work. The image itself starts on less, which is what the second figure is.

--fit caps it to the hostA start given --fit trims each step to what the machine actually has, for that start alone. The definition is never rewritten.

Machines that fit it

FastQC asks for 4 cores and 4 GB. Cheapest first.

E2 Highcpu-4

$0.124/ hour4 cores · 4 GBStart this machine

E2 Standard-4

$0.168/ hour4 cores · 16 GBStart this machine

B4ms

$0.208/ hour4 cores · 16 GBStart this machine

Run FastQC on your own machinePick a machine that meets it, and it opens about a minute after you ask.

Start a machine Browse workflows