PARAMETERS.md

Parameters

A list of all possible parameter that can be used for the different scripts included in Sarek.

Common for all scripts

--help

Display help

--noReports

Disable all QC tools and MultiQC.

--outDir

Choose an output directory

--project ProjectID

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

--publishDirMode

Specify wich mode publishDir directive need to follow, in Sarek link is the default mode.

From Nextflow documentation:

Mode	Description
copy	Copies the output files into the published directory
copyNoFollow	Copies the output files into the published directory without following symlinks ie. copies the links themselves
link	Creates a hard link in the published directory for each process output file (default)
move	Moves the output files into the published directory. Note: this is only supposed to be used for a terminating process i.e. a process whose output is not consumed by any other downstream process
rellink	Creates a relative symbolic link in the published directory for each process output file
symlink	Creates an absolute symbolic link in the published directory for each process output file

--sample file.tsv

Use the given TSV file as sample (cf TSV documentation). Is not used for annotate.nf and runMultiQC.nf.

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

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

• haplotypecaller (use HaplotypeCaller for VC) (germlineVC.nf)
• manta (use Manta for SV) (germlineVC.nf,somaticVC.nf)
• strelka (use Strelka for VC) (germlineVC.nf,somaticVC.nf)
• ascat (use ASCAT for CNV) (somaticVC.nf)
• mutect2 (use MuTect2 for VC) (somaticVC.nf)
• snpeff (use snpEff for Annotation) (annotate.nf)
• vep (use VEP for Annotation) (annotate.nf)

--tools option is case insensitive to avoid easy introduction of errors when choosing tools. So you can write --tools mutect2,ascat or --tools MuTect2,ASCAT without worrying about case sensitivity.

--awsqueue BatchQueueName

Only required if you use the awsbatch profile. This parameter specifies the queue for which jobs are submitted in AWS Batch.

--awsqueue_tiny BatchQueueName

Only used if you use the awsbatch profile. This parameter specifies a queue used for certain small jobs that might still require a significant amount of disk storage.

--localReportDir Directory

Only used if you use the awsbatch profile. This parameter specifies an output directory for nextflow reports, such as Sarek_timeline.html, which currently is not fully supported to store on s3.

Preprocessing script (main.nf)

--step step

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

• mapping (default, will start workflow with FASTQ files)
• recalibrate (will start workflow with BAM files and Recalibration Tables

--step option is case insensitive to avoid easy introduction of errors when choosing a step.

--test

Test run Sarek on a smaller dataset, that way you don't have to specify --sample Sarek-data/testdata/tsv/tiny.tsv

--onlyQC

Run only QC tools and MultiQC to generate a HTML report.

Annotate script (annotate.nf)

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

Choose which tools to annotate. Different tools to be separated by commas. Possible values are:

• haplotypecaller (Annotate HaplotypeCaller output)
• manta (Annotate Manta output)
• mutect2 (Annotate MuTect2 output)
• strelka (Annotate Strelka output)

--annotateVCF file1[,file2,file3...]

Choose vcf to annotate. Different vcfs to be separated by commas.

--annotate_cache

Use available cache on local machine. Works only when used with --snpEff_cache and/or --vep_cache to specify the cache directories. See annotation documentation for more information.

--snpEff_cache /Path/To/snpEffCache

Specify the location of snpEff cache. Works only when used with --annotate_cache. See annotation documentation for more information.

--vep_cache /Path/To/VEPcache

Specify the location of VEP cache. Works only when used with --annotate_cache. See annotation documentation for more information.

MultiQC script (runMultiQC.nf)

--callName Name

Specify a name for MultiQC report (optional)

--contactMail email

Specify an email for MultiQC report (optional)

References

For most use cases, the reference information is already in the configuration file conf/genomes.config. However, if needed, you can specify any reference file at the command line.

--acLoci acLoci file

--bwaIndex bwaIndex file

--dbsnp dbsnp file

--dbsnpIndex dbsnpIndex file

--genomeDict genomeDict file

--genomeFile genomeFile file

--genomeIndex genomeIndex file

--intervals intervals file

--knownIndels knownIndels file

--knownIndelsIndex knownIndelsIndex file

--snpeffDb snpeffDb file

Hardware Parameters

For most use cases, the reference information is already in the appropriate configuration files. However, it is still possible to specify these parameters at the command line as well.

--runTime time

--singleCPUMem memory

--totalMemory memory