Parameters

March 1, 2019 · View on GitHub

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

Common for all scripts

--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.

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.