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Usage

I would recommand to run Nextflow within a screen or tmux session. It is recommanded to run only one instance of CAW for one patient in the same directory. The typical reduced command line is:

nextflow run SciLifeLab/CAW --sample <file.tsv> --step <step> --tools <tool>

All parameters, options and variables can be specified with configuration files and profile (cf configuration documentation).

Options

--callName Name

Specify a name for MultiQC report (optionnal)

--contactMail email

Specify an email for MultiQC report (optionnal)

--help

Display help

--project ProjectID

Specify a project number ID on a UPPMAX cluster. (optionnal if not on such a cluster)

--sample file.tsv

Use the given TSV file as sample (cf TSV documentation).

--step step

Choose from wich step the workflow will start. Choose only one step. Possible values are:

  • preprocessing (default, will start workflow with FASTQ files)
  • realign (will start workflow with BAM files (with T/N BAMs that were not realigned together))
  • recalibrate (will start workflow with BAM files and Recalibration Tables (Only with T/N BAMs that were realigned together))
  • skipPreprocessing (will skip entire preprocessing (Only with T/N BAMs that were realigned together))

--test

Test run CAW on a smaller dataset, that way you don't have to specify --sample data/tsv/tiny.tsv --intervals repeats/tiny.list

--tools tool1[,tool2,tool3...]

Choose which tools will be used in the workflow. Different tools to be separated by commas. Possible values are:

  • Ascat (use ascat for CNV)
  • HaplotypeCaller (use HaplotypeCaller for VC)
  • Manta (use Manta for SV)
  • MultiQC (Make a QC report)
  • MuTect1 (use MuTect1 for VC)
  • MuTect2 (use MuTect2 for VC)
  • Strelka (use Strelka for VC)
  • VarDict (use VarDict for VC)
  • snpEff (use snpEff for Annotation)
  • VEP (use VEP for Annotation)

--verbose

Display more information about files being processed.

--version

Display version number and information.

Parameters

Simpler to specify in the config file.

--runTime time

--singleCPUMem memory

References [(cf References documentation)]

Could be usefull if you wish to change one reference for testing.

--acLoci file

COSMIC files

  • --cosmic file
  • --cosmicIndex file

Files from the GATK Bundle

  • --dbsnp file
  • --dbsnpIndex file
  • --kgIndels file
  • --kgIndex file
  • --genome file
  • --genomeDict file
  • --genomeIndex file
  • --millsIndels file
  • --millsIndex file

BWA indexes

  • --genomeAmb file
  • --genomeAnn file
  • --genomeBwt file
  • --genomePac file
  • --genomeSa file

--intervals file

--snpeffDb db

Which database to use for snpEff

--vardictHome path

Path to Vardict

Nextflow options

See the options documentation

Profiles

More informations on the SciLifeLab Nextflow documentation. The default profile is standard. You can use your own profile:

nextflow run SciLifeLab/CAW --sample mysample.tsv -profile myprofile

A standard profile is defined in nextflow.config. You can use the files in the configuration/ directory as a base to make a new .config file that you can specify directly (or add as a profile):

nextflow run SciLifeLab/CAW --sample mysample.tsv -c config/milou.config

Update to latest version

To update workflow to the latest version use:

nextflow pull SciLifeLab/CAW

Run the latest version

If there is a feature or bugfix you want to use in a resumed or re-analyzed run, you have to update the workflow to the latest version. By default it is not updated automatically, so use something like:

nextflow run -latest SciLifeLab/CAW --sample mysample.tsv -resume