All Modules#

This is an auto-generated list of all modules with links to auto-generated module documentation.

AddMetadataToPathwayTables
AddMetadataToTaxaTables - Map metadata onto taxa tables using sample ID.
AddPseudoCount - Add a pseudocount (+1) to each value in each taxa table.
AwkFastaConverter - Convert fastq files into fasta format.
BuildQiimeMapping
BuildTaxaTables - Convert OTU-tables split by sample into taxa tables split by level.
CompileOtuCounts
DESeq2 - Determine statistically significant differences using DESeq2.
Demultiplexer - Demultiplex samples into separate files for each sample.
EdgeR - Determine statistically significant differences using edgeR.
Email - Send an email containing the pipeline summary when the pipeline either completes or fails.
ForEachFile - Like GenMod, but done for each file in a previous module's output dir.
ForEachLevel - Like GenMod, but done for each taxonomic level.
ForEachLoop - Like GenMod, but done for each string in a comma-separated list.
ForEachSample - Like GenMod, but done for each sample listed in the metadata.
GenMod - Allows user to add their own scripts into the BioLockJ pipeline.
GenomeAssembly - Assemble WGS sequences with MetaSPAdes, bin contigs with Metabat2 and check quality with checkM.
Gunzipper - Decompress gzipped files.
HUMAnN2 - Profile the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.
Hello_Friends - Print the classic phrase: hello world. With some variation.
Hello_World - Print the classic phrase: Hello World!
Humann2Parser - Build OTU tables from HumanN2 classifier module output.
ImportMetadata - Read existing metadata file, or create a default one.
JsonReport
KneadData - Run the Biobakery KneadData program to remove contaminated DNA.
Kraken2Classifier - Classify WGS samples with KRAKEN 2.
Kraken2Parser - Build OTU tables from KRAKEN mpa-format reports.
KrakenClassifier - Classify WGS samples with KRAKEN.
KrakenParser - Build OTU tables from KRAKEN mpa-format reports.
LogTransformTaxaTables - Log-transform the raw taxa counts on Log10 or Log-e scales.
MergeQiimeOtuTables
Metaphlan2Classifier - Classify WGS samples with MetaPhlAn2.
Metaphlan2Parser
Multiplexer - Multiplex samples into a single file, or two files (one with forward reads, one with reverse reads) if multiplexing paired reads.
NormalizeByReadsPerMillion - new counts = counts / (total counts in sample / 1 million)
NormalizeTaxaTables - Normalize taxa tables for sequencing depth.
PearMergeReads - Run pear, the Paired-End reAd mergeR
QiimeClassifier
QiimeClosedRefClassifier - Pick OTUs using a closed reference database and construct an OTU table via the QIIME script pick_closed_reference_otus.py
QiimeDeNovoClassifier - Run the QIIME pick_de_novo_otus.py script on all fasta sequence files
QiimeOpenRefClassifier - Run the QIIME pick_open_reference_otus.py script on all fasta sequence files
QiimeParser
R_CalculateStats - Generate a summary statistics table with [adjusted and unadjusted] [parameteric and non-parametirc] p-values and r² values for each reportable metadata field and each report.taxonomyLevel configured.
R_PlotEffectSize - Generate horizontal barplot representing effect size (Cohen's d, r², and/or fold change) for each reportable metadata field and each report.taxonomyLevel configured.
R_PlotMds - Generate sets of multidimensional scaling plots showing 2 axes at a time (up to the <r_PlotMds.numAxis>th axis) with color coding based on each categorical metadata field (default) or by each field given in r_PlotMds.reportFields
R_PlotOtus - Generate OTU-metadata box-plots and scatter-plots for each reportable metadata field and each report.taxonomyLevel configured
R_PlotPvalHistograms - Generate p-value histograms for each reportable metadata field and each report.taxonomyLevel configured
RarefyOtuCounts - Applies a mean iterative post-OTU classification rarefication algorithm so that each output sample will have approximately the same number of OTUs.
RarefySeqs - Randomly sub-sample sequences to reduce all samples to the configured maximum.
RdpClassifier - Classify 16s samples with RDP.
RdpHierParser - Create taxa tables from the _hierarchicalCount.tsv files output by RDP.
RdpParser - Build OTU tables from RDP reports.
RegisterNumReads
RemoveLowOtuCounts - Removes OTUs with counts below report.minCount.
RemoveLowPathwayCounts
RemoveScarceOtuCounts
RemoveScarcePathwayCounts
Rmarkdown - Render a custom R markdown.
SeqFileValidator - This BioModule validates fasta/fastq file formats are valid and enforces min/max read lengths.
ShannonDiversity - Calculate shannon diversity as sum p(logp)
SraDownload - SraDownload downloads and compresses short read archive (SRA) files to fastq.gz
SraMetaDB - Makes sure that the SRAmetadb exists, downloads if it does not already exist.
SraMetaData - Extract metadata via pysradb from local copy of SRAmetadb.sqlite.
SrpSrrConverter - Create an SraAccList.txt file from an SRA project identifier.
Step5 - Print the classic phrase: hello world.
Stop - Stop a pipeline.
TrimPrimers - Remove primers from reads, option to discard reads unless primers are attached to both forward and reverse reads.