nf-core/rnadnavar
Pipeline for RNA and DNA integrated analysis for somatic mutation detection
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string
Automatic retrieval for restart
string
^\S+\.csv$
Specify how many reads each split of a FastQ file contains. Set 0 to turn off splitting at all.
integer
50000000
Starting step
string
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Save mapped files.
boolean
Save mapped BAMs.
boolean
Saves output from Markduplicates & Baserecalibration as BAM file instead of CRAM
boolean
True if there are RNA samples to be analysed
boolean
true
True if there are DNA samples to be analysed
boolean
true
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
GRCh38
Path to BWA mem indices.
string
Path to bwa-mem2 mem indices.
string
Path to dragmap indices.
string
Path to STAR index folder or compressed file (tar.gz)
string
Splice sites file required for HISAT2.
string
Path to STAR index folder or compressed file (tar.gz)
string
Enable STAR 2-pass mapping mode.
boolean
Do not use GTF file during STAR index buidling step
boolean
Option to limit RAM when sorting BAM file. Value to be specified in bytes. If 0, will be set to the genome index size.
integer
Specifies the number of genome bins for coordinate-sorting
integer
50
Specifies the maximum number of collapsed junctions
integer
1000000
Read length
number
76
Estimate interval size.
number
200000
Path to dbsnp file.
string
Path to dbsnp index.
string
Path to FASTA dictionary file.
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Path to FASTA reference index.
string
Path to GATK Mutect2 Germline Resource File.
string
Path to GATK Mutect2 Germline Resource Index.
string
Path to known indels file.
string
Path to known indels file index.
string
If you use AWS iGenomes, this has already been set for you appropriately.
Path to known snps file.
string
Path to known snps file snps.
string
VEP genome.
string
VEP species.
string
VEP cache version.
number
Save built references.
boolean
Only built references.
boolean
Download annotation cache.
boolean
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes/
Do not load the iGenomes reference config.
boolean
Minimum memory required to use splice sites and exons in the HiSAT2 index build process.
string
200.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Path to GTF annotation file.
string
Path to GFF3 annotation file.
string
Path to BED file containing exon intervals. This will be created from the GTF file if not specified.
string
Trim fastq file or handle UMIs
Run FastP for read trimming
boolean
Remove bp from the 5’ end of read 1
integer
Remove bp from the 5’ end of read 2
integer
Remove bp from the 3’ end of read 1
integer
Remove bp from the 3’ end of read 2
integer
Removing poly-G tails.
integer
Save trimmed FastQ file intermediates.
boolean
If set, publishes split FASTQ files. Intended for testing purposes.
boolean
Define parameters that control the stages in the pipeline
Tools to use for variant calling and/or for annotation.
string
Disable specified tools.
string
Enable when exome or panel data is provided.
boolean
Define parameters related to read alignment
Specify aligner to be used to map reads to reference genome.
string
Where possible, save unaligned reads from aligner to the results directory.
boolean
Save the intermediate BAM files from the alignment step.
boolean
Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.
boolean
Variant callers used to generate calls
string
sage,strelka,mutect2
Specify whether to remove duplicates from the BAM during Picard MarkDuplicates step.
boolean
Disable usage of intervals.
boolean
Path to target bed file in case of whole exome or targeted sequencing or intervals file.
string
Number of times the gene interval list to be split in order to run GATK haplotype caller in parallel
integer
25
Panel-of-normals VCF (bgzipped) for GATK Mutect2
string
Index of PON panel-of-normals VCF.
string
Runs Mutect2 in joint (multi-sample) mode for better concordance among variant calls of tumor samples from the same patient. Mutect2 outputs will be stored in a subfolder named with patient ID under variant_calling/mutect2/
folder. Only a single normal sample per patient is allowed. Tumor-only mode is also supported.
boolean
Bed file with known high confidence used as input in Sage variant caller
string
Bed file with ac actionable list of variants used as input in Sage variant caller
string
Known hotspots used as input in Sage variant caller
string
Directory or tar.gz to ensembl cache for SAGE
string
Directory or tar.gz file to SAGE resources
string
Custom parameters for SAGE
string
Do not analyze soft clipped bases in the reads for GATK Mutect2.
boolean
Allow usage of fasta file for annotation with VEP
boolean
Enable the use of the VEP dbNSFP plugin.
boolean
Path to dbNSFP processed file.
string
Path to dbNSFP tabix indexed file.
string
Consequence to annotate with
string
Fields to annotate with
string
rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF
Enable the use of the VEP LOFTEE plugin.
boolean
Enable the use of the VEP genesplicer plugin.
boolean
Enable the use of the VEP SpliceAI plugin.
boolean
Path to spliceai raw scores snv file.
string
Path to spliceai raw scores snv tabix indexed file.
string
Path to spliceai raw scores indel file.
string
Path to spliceai raw scores indel tabix indexed file.
string
Enable the use of the VEP SpliceRegion plugin.
boolean
Add an extra custom argument to VEP.
string
--no_progress --offline --shift_hgvs 1 --check_existing --tsl --domains --total_length --allele_number --no_escape --xref_refseq --failed 1 --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --format vcf --biotype --force_overwrite --sift p --polyphen p --variant_class --regulatory --allele_number --af_gnomad --af_gnomadg --gene_phenotype --hgvs --hgvsg --max_af
Path to VEP cache.
string
The output directory where the cache will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
VEP output-file format.
string
Path to BED file with variants to whitelist during filtering
string
Path to BED file with positions to blacklist during filtering (e.g. regions difficult to map)
string
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Base path / URL for data used in the test profiles
string
https://raw.githubusercontent.com/nf-core/test-datasets/rnadnavar
Sequencing center information to be added to read group (CN field).
string
Sequencing platform information to be added to read group (PL field).
string
ILLUMINA
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|d|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Email address for completion summary, only when pipeline fails.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Send plain-text email instead of HTML.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Validation of parameters fails when an unrecognised parameter is found.
boolean
Validation of parameters in lenient more.
boolean
Incoming hook URL for messaging service
string
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/