nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
1.1.3). The latest
stable release is
2.14.0
.
Folder containing paired-end demultiplexed FastQ files
stringForward primer sequence
stringReverse primer sequence
stringPath to metadata sheet, when missing most downstream analysis are skipped (barplots, PCoA plots, …).
stringIf samples were sequenced in multiple sequencing runs
booleanPath to ta- separated table with sample IDs, forward and reverse sequencing files
stringCutadapt will retain untrimmed reads, choose only if input reads are not expected to contain primer sequences.
booleanDADA2 read truncation value for forward strand
integerDADA2 read truncation value for reverse strand
integerIf —trunclenf and —trunclenr are not set, these values will be automatically determined using this median quality score
integer25Assures that values chosen with —trunc_qmin will retain a fraction of reads.
number0.75Path to the qiime compatible file Silva_132_release.zip
stringhttps://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_132_release.zipPath to QIIME2 trained classifier file (typically *-classifier.qza)
stringRemove all hash signs from taxonomy strings, resolves a rare ValueError during classification (process classifier)
booleanDereplication of the database. Must bematching SILVA v132 and its subfolders. Database size is descreasing, but taxonomical assignments as well.
integer99Comma separated list of unwanted taxa, to skip taxa filtering use “none”
stringmitochondria,chloroplastAbundance filtering
integer1Prevalence filtering
integer1Define where the pipeline should find input data and save output data.
Path to test sequencing read files
stringComma separated list of metadata column headers for statistics.
stringIf the sequencing data has PHRED 64 encoded quality scores, otherwise PHRED 33 is assumed
booleanA string that will be used between the prepended run/folder name and the sample name. Only used with “—multipleSequencingRuns”.
string-Naming of sequencing files
string/*_R{1,2}_001.fastq.gzThe output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Needs to be specified to resolve a timezone error
stringEurope/BerlinKeep additional intermediate files, such as trimmed reads or various QIIME2 archives
booleanSkip all steps after importing into QIIME2, used for visually choosing DADA2 parameter --trunclenf and --trunclenr
booleanPath to imported reads (e.g. “demux.qza”)
stringSkip all steps after denoising, produce only sequences and abundance tables on ASV level
booleanSkip FastQC
booleanSkip alpha rarefaction
booleanSkip producing barplot
booleanSkip taxonomic classification
booleanSkip producing any relative abundance tables
booleanSkip alpha and beta diversity analysis
booleanSkip differential abundance testing
booleanSkip MultiQC reporting
booleanLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringWorkflow name.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoParameters 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 configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringstringstringeu-west-1string