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USAGE.md

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Usage

I would recommand to run Nextflow within a screen session (cf help on screen). It is recommanded to run only one instance of CAW for one patient in the same directory. Meaning there should be only one patient analysed in one directory. The typical command line is:

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

All variables and parameters are specified in the config (cf configuration documentation).

All samples are specified in the TSV files (cf TSV documentation).

Steps

Steps are used to configure which processes will be runned or skipped in the workflow. Different steps to be separated by commas. 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))
  • skipPreprocessing (will skip entire preprocessing (Only with T/N BAMs that were realigned together))
  • MuTect1 (use MuTect1 for VC)
  • MuTect2 (use MuTect2 for VC)
  • VarDict (use VarDict for VC)
  • Strelka (use Strelka for VC)
  • HaplotypeCaller (use HaplotypeCaller for normal bams VC)
  • Manta (use Manta for SV)
  • Ascat (use ascat for CNV)
  • MultiQC (Make a QC report)

Project

To specify your UPPMAX project number ID. It can also be specified in your config file (cf configuration documentation).

nextflow run SciLifeLab/CAW --sample <file.tsv> --project <UPPMAX_Project>

Verbose

To have more information about files being processed, you can use the verbose option:

nextflow run SciLifeLab/CAW --sample mysample.tsv --verbose

Test

To test CAW and run it on smaller dataset, use one of the following option:

  • --test will test step preprocessing on tiny test data.
  • --testRealign will test step realign on tiny test data. Need to run nextflow run SciLifeLab/CAW --test before.
  • --testCoreVC will test steps skipPreprocessing, MuTect1, Strelka and HaplotypeCaller on tiny test data. Need to run nextflow run SciLifeLab/CAW --test before.
  • --testSideVC will test steps skipPreprocessing, Ascat, Manta and HaplotypeCaller on test downsampled set.

Nextflow options

See the options documentation

Profiles

More informations on the SciLifeLab Nextflow documentation. The default profile is standard. If you want 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 config/milou.config file 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