nf-core/eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
22.10.6.
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Define where the pipeline should find input data and save output data.
Path to tab- or comma-separated file containing information about the samples in the experiment.
string^\S+\.(c|t)sv$Specify to convert input BAM files back to FASTQ for remapping
booleanThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Path to FASTA file of the reference genome.
string^\S+\.fn?a(sta)?(\.gz)?$Specify path to samtools FASTA index.
stringSpecify path to Picard sequence dictionary file.
stringSpecify path to directory containing index files of the FASTA for a given mapper.
stringSpecify to generate ‘.csi’ BAM indices instead of ‘.bai’ for larger reference genomes.
booleanSpecify to save any pipeline-generated reference genome indices in the results directory.
booleanPath to a tab-/comma-separated file containing reference-specific files.
string^\S+\.(c|t)sv$Name of iGenomes reference.
stringDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanSpecify the FASTA header of the extended chromosome when using circularmapper.
stringSpecify the number of bases to extend reference by (circularmapper only).
integer500Specify an elongated reference FASTA to be used for circularmapper.
stringSpecify a samtools index for the elongated FASTA file.
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.
stringLess 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, 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.
booleanIncoming hook URL for messaging service
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
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringRemoval of adapters, paired-end merging, poly-G removal, etc.
Specify which tool to use for sequencing quality control.
stringSpecify to skip all preprocessing steps (adapter removal, paired-end merging, poly-G trimming, etc).
booleanSpecify which preprocessing tool to use.
stringSpecify to skip read-pair merging.
booleanSpecify to exclude read-pairs that did not overlap sufficiently for merging (i.e., keep merged reads only).
booleanSpecify to skip removal of adapters.
booleanSpecify the nucleotide sequence for the forward read/R1.
stringSpecify the nucleotide sequence for the reverse read/R2.
stringSpecify a list of all possible adapters to trim.
stringSpecify the minimum length reads must have to be retained.
integer25Specify number of bases to hard-trim from 5 prime or front of reads.
integerSpecify number of bases to hard-trim from 3 prime or tail of reads.
integerSpecify to save the preprocessed reads in the results directory.
booleanSpecify to turn on sequence complexity filtering of reads.
booleanSpecify the complexity threshold that must be reached or exceeded to retain reads.
integer10Skip AdapterRemoval quality and N base trimming at 5 prime end.
booleanSpecify to skip AdapterRemoval quality and N trimming at the ends of reads.
booleanSpecify AdapterRemoval minimum base quality for trimming off bases.
integer20Specify to skip AdapterRemoval N trimming (quality trimming only).
booleanSpecify the AdapterRemoval minimum adapter overlap required for trimming.
integer1Specify the AdapterRemoval maximum Phred score used in input FASTQ files.
integer41Options for aligning reads against reference genome(s)
Specify to turn on FASTQ sharding.
booleanSpecify the number of reads in each shard when splitting.
integer1000000Specify which mapper to use.
stringSpecify the amount of allowed mismatches in the alignment for mapping with BWA aln.
number0.01Specify the maximum edit distance allowed in a seed for mapping with BWA aln.
integer2Specify the length of seeds to be used for BWA aln.
integer1024Specify the number of gaps allowed for alignment with BWA aln.
integer2Specify the minimum seed length for alignment with BWA mem.
integer19Specify the re-seeding threshold for alignment with BWA mem.
number1.5Specify the Bowtie 2 alignment mode.
stringSpecify the level of sensitivity for the Bowtie 2 alignment mode.
stringSpecify the number of mismatches in seed for alignment with Bowtie 2.
integerSpecify the length of seed substrings for Bowtie 2.
integer20Specify the number of bases to trim off from 5 prime end of read before alignment with Bowtie 2.
integerSpecify the number of bases to trim off from 3 prime end of read before alignment with Bowtie 2.
integerSpecify the maximum fragment length for Bowtie2 paired-end mapping mode only.
integer500Turn on to remove reads that did not map to the circularised genome.
booleanSpecify the -p parameter for mapAD, i.e. mismatch budget for the alignment.
number0.03Specify the -f parameter for mapAD, which sets the 5’-overhang length parameter of mapAD’s aDNA scoring model.
number0.5Specify the -t parameter for mapAD, which sets the 3’-overhang length parameter of mapAD’s aDNA scoring model.
number0.5Specify the -d parameter for mapAD, which sets the double-stranded deamination rate parameter of mapAD’s aDNA scoring model.
number0.02Specify the -s parameter for mapAD, which sets the single-stranded deamination rate parameter of mapAD’s aDNA scoring model.
number1Specify the -i parameter for mapAD, which adjusts the expected indel rate between reads and reference.
number0.001Specify the -x parameter for mapAD, which adjusts the gap extension penalty.
number0.5Specify the —gap_dist_ends parameter for mapAD, which defines the distance from the read ends in which no gaps are permitted.
number5Specify the number of gaps allowed for alignment with mapAD.
number2Specify the base error rate parameter for mapAD.
number0.02Set the —ignore_base_quality flag, which instructs mapAD to ignore base quality values in its scoring model.
booleanSet the —no_search_limit_recovery flag, which instructs mapAD to abort instead of trying to recover from full internal data structures.
booleanOptions related to length, quality, and map status filtering of reads.
Specify to turn on filtering of reads in BAM files after mapping. By default, only mapped reads retained.
booleanSpecify the minimum read length mapped reads should have for downstream genomic analysis.
integerSpecify the minimum mapping quality reads should have for downstream genomic analysis.
integerSpecify the SAM format flag of reads to remove during BAM filtering for downstream genomic steps.
integer4Specify to retain unmapped reads in the BAM file used for downstream genomic analyses.
booleanSpecify to generate FASTQ files from the filtered BAM files.
booleanSpecify to save the intermediate filtered genomic BAM files in the results directory.
booleanOptions related to metagenomic screening.
Specify to turn on metagenomic screening of mapped, unmapped or all reads.
booleanSpecify which type of reads to use for metagenomic screening.
stringSpecify to turn on saving of input for metagenomics.
booleanSpecify to run a complexity filter on the metagenomics input files before classification.
booleanSpecify to save FASTQ files containing the complexity-filtered reads before metagenomic classification.
booleanSpecify which tool to use for trimming, filtering or reformatting of FASTQ reads that go into metagenomics screening.
stringSpecify the entropy threshold under which a sequencing read will be complexity-filtered out.
number0.3Specify the complexity filter mode for PRINSEQ++.
stringSpecify the minimum dust score for PRINTSEQ++ complexity filtering
number0.5Specify which tool to use for metagenomic profiling and screening. Required if --run_metagenomics flagged.
stringSpecify a databse directory or .tar.gz file of a database directory to run metagenomics profiling on. Required if --run_metagenomics flagged.
stringTurn on saving reads assigned by KrakenUniq or Kraken2
booleanTurn on saving of KrakenUniq or Kraken2 per-read taxonomic assignment file
booleanSpecify how large to chunk database when loading into memory for KrakenUniq
string16GTurn on saving minimizer information in the kraken2 report thus increasing to an eight column layout.
booleanSpecify which alignment mode to use for MALT.
stringSpecify alignment method for MALT.
stringPercent identity value threshold for MALT.
integer85Specify the percent for LCA algorithm for MALT (see MEGAN6 CE manual).
integer1Specify whether to use percent or raw number of reads for minimum support required for taxon to be retained for MALT.
stringSpecify the minimum percentage of reads a taxon of sample total is required to have to be retained for MALT.
number0.01Specify a minimum number of reads a taxon of sample total is required to have to be retained in malt or kraken. Not compatible with —malt_min_support_mode ‘percent’.
integer1Specify the maximum number of queries a read can have for MALT.
integer100Specify the memory load method. Do not use ‘map’ with GPFS file systems for MALT as can be very slow.
stringSpecify to also produce SAM alignment files. Note this includes both aligned and unaligned reads, and are gzipped. Note this will result in very large file sizes.
booleanDefine how many fastq files should be submitted in the same malt run. Default value of 0 runs all files at once.
integerActivate post-processing of metagenomics profiling tool selected.
booleanPath to a text file with taxa of interest (one taxon per row, NCBI taxonomy name format)
stringPath to directory containing containing NCBI resource files (ncbi.tre and ncbi.map; available: https://github.com/rhuebler/HOPS/)
stringSpecify which MaltExtract filter to use.
stringSpecify percent of top alignments to use.
number0.01Turn off destacking.
booleanTurn off downsampling.
booleanTurn off duplicate removal.
booleanTurn on exporting alignments of hits in BLAST format.
booleanTurn on export of MEGAN summary files.
booleanMinimum percent identity alignments are required to have to be reported as candidate reads. Recommended to set same as MALT parameter.
number85Turn on using top alignments per read after filtering.
booleanOptions for removal of PCR duplicates
Specify to skip the removal of PCR duplicates.
booleanSpecify which tool to use for deduplication.
stringOptions for filtering for, trimming or rescaling characteristic ancient DNA damage patterns
Specify to turn on damage rescaling of BAM files using mapDamage2 to probabilistically remove damage.
booleanSpecify the length of read sequence to use from each side for rescaling.
integer12Specify the length of read for mapDamage2 to rescale from 5 prime end.
integerSpecify the length of read for mapDamage2 to rescale from 3 prime end.
integerSpecify to turn on PMDtools filtering.
booleanSpecify PMD score threshold for PMDtools.
integer3Specify a masked FASTA file with positions to be used with PMDtools.
string^\S+\.fa?(\sta)$Specify a BED file to be used to mask the reference FASTA prior to running PMDtools.
string^\S+\.bed?(\.gz)$Specify to turn on BAM trimming for non-UDG or half-UDG libraries.
booleanSpecify the number of bases to clip off reads from ‘left’ (5 prime) end of reads for double-stranded non-UDG libraries.
integerSpecify the number of bases to clip off reads from ‘right’ (3 prime) end of reads for double-stranded non-UDG libraries.
integerSpecify the number of bases to clip off reads from ‘left’ (5 prime) end of read for double-stranded half-UDG libraries.
integerSpecify the number of bases to clip off reads from ‘right’ (3 prime) end of read for double-stranded half-UDG libraries.
integerSpecify the number of bases to clip off reads from ‘left’ (5 prime) end of read for single-stranded non-UDG libraries.
integerSpecify the number of bases to clip off reads from ‘right’ (3 prime) end of read for single-stranded non-UDG libraries.
integerSpecify the number of bases to clip off reads from ‘left’ (5 prime) end of read for single-stranded half-UDG libraries.
integerSpecify the number of bases to clip off reads from ‘right’ (3 prime) end of read for single-stranded half-UDG libraries.
integerSpecify to turn on soft-trimming instead of hard masking.
booleanOptions for variant calling
Specify to turn on genotyping of BAM files.
booleanSpecify which input BAM to use for genotyping.
stringSpecify which genotyper to use.
stringSpecify to skip generation of VCF-based variant calling statistics with bcftools.
booleanSpecify the ploidy of the reference organism.
integer2Specify the base mapping quality to be used for genotyping with pileupCaller.
integer30Specify the minimum mapping quality to be used for genotyping with pileupCaller.
integer30Specify the path to SNP panel in BED format for pileupCaller.
stringSpecify the path to SNP panel in EIGENSTRAT format for pileupCaller.
stringSpecify the SNP calling method to use for genotyping with pileupCaller.
stringSpecify the calling mode for transitions with pileupCaller.
stringSpecify GATK phred-scaled confidence threshold.
integer30Specify VCF file for SNP annotation of output VCF files for GATK.
string^\S+\.vcf$Specify the maximum depth coverage allowed for genotyping with GATK before down-sampling is turned on.
integer250Specify GATK UnifiedGenotyper output mode.
stringSpecify UnifiedGenotyper likelihood model.
stringSpecify to keep the BAM output of re-alignment around variants from GATK UnifiedGenotyper.
booleanSpecify to supply a default base quality if a read is missing a base quality score.
integer-1Specify GATK HaplotypeCaller output mode.
stringSpecify HaplotypeCaller mode for emitting reference confidence calls.
stringSpecify minimum required supporting observations of an alternate allele to consider a variant in FreeBayes.
integer1Specify to skip over regions of high depth by discarding alignments overlapping positions where total read depth is greater than specified in FreeBayes.
integerSpecify which ANGSD genotyping likelihood model to use.
stringSpecify the formatting of the output VCF for ANGSD genotype likelihood results.
stringOptions for the calculation of ratio of reads to one chromosome/FASTA entry against all others.
Specify to turn on mitochondrial to nuclear ratio calculation.
booleanSpecify the name of the reference FASTA entry corresponding to the mitochondrial genome.
stringMTOptions for the calculation of mapping statistics
Specify to turn off the computation of library complexity estimation with preseq.
booleanSpecify which mode of preseq to run.
stringSpecify the step size (i.e., sampling regularity) of preseq.
integer1000Specify the maximum number of terms that preseq’s lc_extrap mode will use.
integer100Specify the maximum extrapolation to use for preseq’s lc_extrap mode.
integer10000000000Specify number of bootstraps to perform in preseq’s lc_extrap mode.
integer100Specify confidence interval level for preseq’s lc_extrap mode.
number0.95Specify to turn on preseq defects mode to extrapolate without testing for defects in lc_extrap mode.
booleanSpecify to turn off coverage calculation with Qualimap.
booleanSpecify path to SNP capture positions in BED format for coverage calculations with Qualimap.
stringOptions for calculating and filtering for characteristic ancient DNA damage patterns.
Specify to turn off ancient DNA damage calculation.
booleanSpecify the tool to use for damage calculation.
stringSpecify the maximum misincorporation frequency that should be displayed on damage plot.
number0.3Specify number of bases of each read to be considered for plotting damage estimation.
integer25Specify the length filter for DamageProfiler.
integer100Specify the maximum number of reads to consider for damage calculation with mapDamage.
integerOptions for calculating reference annotation statistics (e.g. gene coverages)
Specify to turn on calculation of number of reads, depth and breadth coverage of features in reference with bedtools.
booleanSpecify path to GFF or BED file containing positions of features in reference file for bedtools.
stringOptions for removing host-mapped reads
Specify to turn on creation of pre-adapter-removal and/or read-pair-merging FASTQ files without reads that mapped to reference (e.g. for public upload of privacy sensitive non-host data).
booleanSpecify the host-mapped read removal mode.
stringOptions for the estimation of contamination in human data
Specify to turn on nuclear contamination estimation for genomes with ANGSD.
booleanSpecify the name of the chromosome to be used for contamination estimation with ANGSD.
stringXSpecify the first position on the chromosome to be used for contamination estimation with ANGSD.
integer5000000Specify the last position on the chromosome to be used for contamination estimation with ANGSD.
integer154900000Specify the minimum mapping quality reads should have for contamination estimation with ANGSD.
integer30Specify the minimum base quality reads should have for contamination estimation with ANGSD.
integer30Specify path to HapMap file of chromosome for contamination estimation with ANGSD.
string${projectDir}/assets/angsd_resources/HapMapChrX.gzOptions for the calculation of genetic sex of human individuals.
Specify to turn on sex determination for genomes mapped to human reference genomes with Sex.DetERRmine.
booleanSpecify path to SNP panel in BED format for error bar calculation.
string