module.seq
Modules from the biolockj.module.seq package prepare sequence data or metadata prior to classification.
If included, seq modules must be ordered to run before modules from any of the other packages.
#BioModule biolockj.module.seq.AwkFastaConverter
Description: Convert fastq files into fasta format (required by QIIME).
- exe.awk
- exe.gzip
#BioModule biolockj.module.seq.Gunzipper
Description: Decompress gzipped files.
- exe.gzip
#BioModule biolockj.module.seq.KneadData
Description: Runs the Biobakery KneadData program to remove contaminated DNA.
- kneaddata.dbs
- exe.kneaddata
- exe.kneaddataParams
#BioModule biolockj.module.seq.Multiplexer
Description: Multiplex samples into a single file, or two files (one with forward reads, one with reverse reads) if multiplexing paired reads.
BioLockJ modules require demultiplexed data, so if included, this must be the last module in the pipeline other than module.report modules.
- metadata.barcodeColumn
- metadata.filePath
#BioModule biolockj.module.seq.PearMergeReads
Description: Merge paired reads (required for RDP & QIIME). For more informations, see the online PEAR manual.
- exe.pear
- exe.pearParams
#BioModule biolockj.module.seq.RarefySeqs
Description: Randomly select samples to reduce all samples to the configured maximum.
Samples with less than the minimum number of reads are discarded.
- rarefySeqs.max
- rarefySeqs.min
#BioModule biolockj.module.seq.SeqFileValidator
Description: This BioModule validates fasta/fastq file formats are valid and enforces min/max read lengths.
- input.seqMaxLen
- input.seqMinLen
#BioModule biolockj.module.seq.TrimPrimers
Description: Remove primers from reads, option to discard reads unless primers are attached to both forward and reverse reads.
- trimPrimers.filePath
- trimPrimers.requirePrimer
BioLockJ: data-wrangling done right.