| Input/output options |
input |
string |
Path to comma-separated file containing information about the samples in the experiment. |
- |
* |
|
primers |
string |
Path to comma-separated file containing forward_primer and reverse_primer sequences. |
- |
|
|
outdir |
string |
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. |
- |
* |
|
email |
string |
Email address for completion summary. |
- |
|
|
multiqc_title |
string |
MultiQC report title. Printed as page header, used for filename if not otherwise specified. |
- |
|
| VSEARCH options |
merge_allowmergestagger |
boolean |
Fastq merge process: allow merging of staggered read pairs. |
- |
|
|
merge_maxdiffs |
integer |
Fastq merge process: Discard input sequences with more bases difference than specified |
30 |
|
|
merge_minlen |
integer |
Fastq merge process: Discard input sequences shorter than the specified number of bases |
0 |
|
|
merge_maxdiffpct |
integer |
Fastq merge process: maximum percentage of non-matching nucleotides allowed in the overlap region |
100 |
|
|
merge_maxlen |
integer |
Fastq merge process: Discard sequences longer than the specified number of bases |
0 |
|
|
filter_maxee |
number |
Filtering process: Discard sequences with an expected error greater than the specified number |
1 |
|
|
filter_maxns |
integer |
Filtering process: Discard sequences with more than the specified number of N’s. |
0 |
|
|
filter_minlen |
integer |
Filtering process: Discard sequences shorter than the specified length. |
0 |
|
|
filter_maxlen |
integer |
Filtering process: Discard sequences longer than the specified length. |
0 |
|
|
derep_strand |
string |
Dereplicate process: plus or both strands |
plus |
|
|
derep_all_strand |
string |
Dereplicate process all samples: plus or both strands |
plus |
|
|
derep_all_fastawidth |
integer |
Dereplicate process all samples: Fasta files produced by vsearch are wrapped, set the value to zero to eliminate the wrapping. |
0 |
|
|
derep_all_minunique |
integer |
Dereplicate process all samples: minimum number of sequences to be defined as unique |
2 |
|
|
cluster_minsize |
integer |
Clustering minsize, set higher to lower number of inferred ASVs, in case of many spurious |
8 |
|
|
cluster_alpha |
number |
Clustering alpha, set lower to lower number of inferred ASVs, in case of many spurious |
2.0 |
|
|
sort_fastawidth |
integer |
Sorting and removing singletons: fastawidth, set to zero to eliminate the wrapping. |
0 |
|
|
sort_minsize |
integer |
Sorting and removing singletons: minsize is default set at 2 to remove singletons. |
2 |
|
|
uchime_label |
string |
Chimera removal: labeling (prefix) of ASVs |
ASV_ |
|
|
usearch_id |
number |
Usearch global: id parameter |
0.97 |
|
| DADA2 options |
dada2_minboot |
integer |
assignTaxonomy function: The minimum bootstrap confidence for assigning a taxonomic level. |
80 |
|
|
dada2_allowmultiple |
integer |
addSpecies function: maximum number of multiple assigned species. If 0, this will be set at FALSE. |
3 |
|
|
dada2_tryrevcompl |
boolean |
addSpecies function: If TRUE, the reverse-complement of each sequences will be used for classification if it is a better match to the reference sequences than the forward sequence. |
true |
|
| Phyloseq options |
rarelevel |
integer |
Rarefaction level (not used if skip_rarefaction is set at true) |
0 |
|
| Skip options |
skip_primers |
boolean |
Skip trimming of primers |
- |
|
|
skip_tree |
boolean |
Skip multiple sequence alignment and tree processes |
- |
|
|
skip_rarefaction |
boolean |
Skip rarefaction of phyloseq object |
- |
|
|
skip_fixtaxonomy |
boolean |
Skip process to make a table with composite taxonomy names |
- |
|
|
skip_metrics |
boolean |
Skip process to provide some general metrics of the phyloseq object (composition, diversity) |
- |
|