nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
1.2.0
). The latest
stable release is
2.14.0
.
Folder containing paired-end demultiplexed FastQ files
string
Forward primer sequence
string
Reverse primer sequence
string
Path to metadata sheet, when missing most downstream analysis are skipped (barplots, PCoA plots, …).
string
If samples were sequenced in multiple sequencing runs
boolean
Path to tab-separated table with sample IDs and paths to sequencing files
string
DADA2 read filtering option
integer
2
DADA2 read filtering option [PacBio only]
integer
2999
DADA2 read filtering option [PacBio only]
integer
50
Cutadapt will retain untrimmed reads, choose only if input reads are not expected to contain primer sequences.
boolean
Cutadapt will be run twice to ensure removal of potential double primers
boolean
DADA2 read truncation value for forward strand, set this to 0 for no truncation
integer
DADA2 read truncation value for reverse strand, set this to 0 for no truncation
integer
If —trunclenf and —trunclenr are not set, these values will be automatically determined using this median quality score
integer
25
Assures that values chosen with —trunc_qmin will retain a fraction of reads.
number
0.75
Path to taxonomic reference database, currently accepts a qiime compatible file Silva_132_release.zip or a UNITE fasta file
string
https://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_132_release.zip
Specify which database to use for taxonomic assignment. Either ‘silva’ or ‘unite’ (default: ‘silva’).
string
silva
Path to QIIME2 trained classifier file (typically *-classifier.qza)
string
Remove all hash signs from taxonomy strings, resolves a rare ValueError during classification (process classifier)
boolean
Dereplication of the database. Must bematching SILVA v132 and its subfolders. Database size is descreasing, but taxonomical assignments as well.
integer
99
Comma separated list of unwanted taxa, to skip taxa filtering use “none”
string
mitochondria,chloroplast
Abundance filtering
integer
1
Prevalence filtering
integer
1
Define where the pipeline should find input data and save output data.
Path to test sequencing read files
string
Comma separated list of metadata column headers for statistics.
string
If PacBio data. Use this option together with —manifest
boolean
If the sequencing data has PHRED 64 encoded quality scores, otherwise PHRED 33 is assumed
boolean
A 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.gz
The output directory where the results will be saved.
string
./results
Email 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
string
Europe/Berlin
Keep additional intermediate files, such as trimmed reads or various QIIME2 archives
boolean
Skip all steps after importing into QIIME2, used for visually choosing DADA2 parameter --trunclenf
and --trunclenr
boolean
Path to imported reads (e.g. “demux.qza”)
string
Skip all steps after denoising, produce only sequences and abundance tables on ASV level
boolean
Skip FastQC
boolean
Skip alpha rarefaction
boolean
Skip producing barplot
boolean
Skip taxonomic classification
boolean
Skip producing any relative abundance tables
boolean
Skip alpha and beta diversity analysis
boolean
Skip differential abundance testing
boolean
Skip MultiQC reporting
boolean
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Method used to save pipeline results to output directory.
string
Workflow name.
string
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
Do not use coloured log outputs.
boolean
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
string
string
string
eu-west-1
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 configs hostname.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
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
Maximum amount of time that can be requested for any single job.
string
240.h