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.
stringAutomatic retrieval for restart
string^\S+\.csv$Specify how many reads each split of a FastQ file contains. Set 0 to turn off splitting at all.
integer50000000Starting step
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringSave mapped files.
booleanSave mapped BAMs.
booleanSaves output from Markduplicates & Baserecalibration as BAM file instead of CRAM
booleanTrue if there are RNA samples to be analysed
booleantrueTrue if there are DNA samples to be analysed
booleantrueReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringGRCh38Path to BWA mem indices.
stringPath to bwa-mem2 mem indices.
stringPath to dragmap indices.
stringPath to STAR index folder or compressed file (tar.gz)
stringSplice sites file required for HISAT2.
stringPath to STAR index folder or compressed file (tar.gz)
stringEnable STAR 2-pass mapping mode.
booleanDo not use GTF file during STAR index buidling step
booleanOption to limit RAM when sorting BAM file. Value to be specified in bytes. If 0, will be set to the genome index size.
integerSpecifies the number of genome bins for coordinate-sorting
integer50Specifies the maximum number of collapsed junctions
integer1000000Read length
number76Estimate interval size.
number200000Path to dbsnp file.
stringPath to dbsnp index.
stringPath to FASTA dictionary file.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to FASTA reference index.
stringPath to GATK Mutect2 Germline Resource File.
stringPath to GATK Mutect2 Germline Resource Index.
stringPath to known indels file.
stringPath to known indels file index.
stringIf you use AWS iGenomes, this has already been set for you appropriately.
Path to known snps file.
stringPath to known snps file snps.
stringVEP genome.
stringVEP species.
stringVEP cache version.
numberSave built references.
booleanOnly built references.
booleanDownload annotation cache.
booleanDo not load the iGenomes reference config.
booleanMinimum memory required to use splice sites and exons in the HiSAT2 index build process.
string200.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Path to GTF annotation file.
stringPath to GFF3 annotation file.
stringTrim fastq file or handle UMIs
Run FastP for read trimming
booleanRemove bp from the 5’ end of read 1
integerRemove bp from the 5’ end of read 2
integerRemove bp from the 3’ end of read 1
integerRemove bp from the 3’ end of read 2
integerRemoving poly-G tails.
integerSave trimmed FastQ file intermediates.
booleanIf set, publishes split FASTQ files. Intended for testing purposes.
booleanDefine parameters that control the stages in the pipeline
Tools to use for variant calling and/or for annotation.
stringDisable specified tools.
stringEnable when exome or panel data is provided.
booleanDefine parameters related to read alignment
Specify aligner to be used to map reads to reference genome.
stringWhere possible, save unaligned reads from aligner to the results directory.
booleanSave the intermediate BAM files from the alignment step.
booleanCreate a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.
booleanVariant callers used to generate calls
stringsage,strelka,mutect2Specify whether to remove duplicates from the BAM during Picard MarkDuplicates step.
booleanDisable usage of intervals.
booleanPath to target bed file in case of whole exome or targeted sequencing or intervals file.
stringNumber of times the gene interval list to be split in order to run GATK haplotype caller in parallel
integer25Panel-of-normals VCF (bgzipped) for GATK Mutect2
stringIndex of PON panel-of-normals VCF.
stringRuns 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.
booleanBed file with known high confidence used as input in Sage variant caller
stringBed file with ac actionable list of variants used as input in Sage variant caller
stringKnown hotspots used as input in Sage variant caller
stringDirectory or tar.gz to ensembl cache for SAGE
stringDirectory or tar.gz file to SAGE resources
stringCustom parameters for SAGE
stringDo not analyze soft clipped bases in the reads for GATK Mutect2.
booleanAllow usage of fasta file for annotation with VEP
booleanEnable the use of the VEP dbNSFP plugin.
booleanPath to dbNSFP processed file.
stringPath to dbNSFP tabix indexed file.
stringConsequence to annotate with
stringFields to annotate with
stringrs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AFEnable the use of the VEP LOFTEE plugin.
booleanEnable the use of the VEP genesplicer plugin.
booleanEnable the use of the VEP SpliceAI plugin.
booleanPath to spliceai raw scores snv file.
stringPath to spliceai raw scores snv tabix indexed file.
stringPath to spliceai raw scores indel file.
stringPath to spliceai raw scores indel tabix indexed file.
stringEnable the use of the VEP SpliceRegion plugin.
booleanAdd 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_afPath to VEP cache.
stringThe output directory where the cache will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringVEP output-file format.
stringThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Path to BED file with positions to blacklist during filtering (e.g. regions difficult to map)
stringPath to BED file with variants to whitelist during filtering
stringPath to BED files with RNA editing sites, comma separated if more than one
stringChain file to do liftover - only if rna_pon2 is provided
stringPath to RNA PoN
stringPath to second RNA PoN
stringPath to second fasta file - only is rna_pon2 provided
stringRNA filtering - name of the second reference being used (e.g. HG19) - only if rna_pon2 is provided
stringRNA filtering - name of the reference being used (e.g. HG38)
stringParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringBase path / URL for data used in the test profiles
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/rnadnavar/Base path / URL for data used in the modules
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Sequencing center information to be added to read group (CN field).
stringSequencing platform information to be added to read group (PL field).
stringILLUMINALess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail 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})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanMultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueIncoming hook URL for messaging service
stringSuffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string