Workflow Elements

This section contains detailed description of all workflow elements presented in the Workflow Designer.

For each element you can find:

• Description of the parameters used in the GUI
• Corresponding parameters names used in a workflow file
• Information about input and output ports

The type of a parameter can be one of the following:

string

A string.

numeric

A number.

boolean

A boolean data type. Available values are: true / false, 0 / 1 and yes / no.

A port’s slot type can be one of the following:

sequence

Biological sequence

msa

Multiple sequence alignment

text

A text

annotation-table

Table of annotations

annotation-table-list

A list of different tables of annotations

ebwt-index

 Bowtie index

hmm2-profile

A HMM profile of HMMER2 package

fmatrix

 Frequency matrix

wmatrix

Weight matrix

sitecon-model

 SITECON model

assembly

Assembly

variation

Variation track

To search an element use the name filter or press the Ctrl+F shortcut that moves you to the name filter also:

• Data Readers
  • Read Alignment Element
  • Read Annotations Element
  • Read FASTQ File with SE Reads Element
  • Read FASTQ Files with PE Reads Element
  • Read File URL(s) Element
  • Read NGS Reads Assembly Element
  • Read Plain Text Element
  • Read Sequence Element
  • Read Sequence from Remote Database Element
  • Read Variants Element
• Data Writers
  • Write Alignment Element
  • Write Annotations Element
  • Write FASTA Element
  • Write NGS Reads Assembly Element
  • Write Plain Text Element
  • Write Sequence Element
  • Write Variants Element
• Data Flow
  • Filter Element
  • Grouper Element
  • Multiplexer Element
  • Sequence Marker Element
• Basic Analysis
  • Amino Translations Element
  • Annotate with UQL Element
  • CD-Search Element
  • Collocation Search Element
  • Export PHRED Qualities Element
  • Fetch Sequences by ID From Annotation Element
  • Filter Annotation by Name Element
  • Filter Annotations by Qualifier
  • Find Correct Primer Pairs Element
  • Find Pattern Element
  • Find Repeats Element
  • Gene-by-gene approach report
  • Get Sequences by Annotations Element
  • Group Primer Pairs Element
  • Import PHRED Qualities Element
  • Intersect Annotations Element
  • Local BLAST Search Element
  • Local BLAST+ Search Element
  • Merge Annotations Element
  • ORF Marker Element
  • Remote BLAST Element
  • Sequence Quality Trimmer Element
  • Smith-Waterman Search Element
• Data Converters
  • Convert bedGraph Files to bigWig Element
  • Convert Text to Sequence Element
  • File Format Conversion Element
  • Reverse Complement Element
  • Split Assembly into Sequences Element
• DNA Assembly
  • Assembly Sequences with CAP3
• HMMER2 Tools
  • HMM2 Build Element
  • HMM2 Search Element
  • Read HMM2 Profile Element
  • Write HMM2 Profile Element
• HMMER3 Tools
  • HMM3 Build Element
  • HMM3 Search Element
  • Read HMM3 Profile
  • Write HMM3 Profile
• Multiple Sequence Alignment
  • Align Profile to Profile with MUSCLE Element
  • Align with ClustalO Element
  • Align with ClustalW Element
  • Align with Kalign Element
  • Align with MAFFT Element
  • Align with MUSCLE Element
  • Align with T-Coffee Element
  • Extract Consensus from Alignment as Sequence
  • Extract Consensus from Alignment as Text
  • In Silico PCR Element
  • Join Sequences into Alignment Element
  • Map to Reference Element
  • Split Alignment into Sequences Element
• NGS: Basic Functions
  • CASAVA FASTQ Filter Element
  • Cut Adapter Element
  • Extract Consensus from Assembly Element
  • Extract Coverage from Assembly Element
  • FASTQ Merger Element
  • FASTQ Quality Trimmer Element
  • FastQC Quality Control Element
  • Filter BAM/SAM Files Element
  • Genome Coverage Element
  • Improve Reads with Trimmomatic Element
  • Merge BAM Files Element
  • Remove Duplicates in BAM Files Element
  • Slopbed Element
  • Sort BAM Files Element
• NGS: ChIP-Seq Analysis
  • Annotate Peaks with peak2gene Element
  • Build Conservation Plot Element
  • Collect Motifs with SeqPos Element
  • Conduct GO Element
  • Create CEAS Report Element
  • Find Peaks with MACS Element
• NGS: Map/Assemble Reads
  • Assemble Reads with SPAdes Element
  • Map Reads with Bowtie Element
  • Map Reads with Bowtie2 Element
  • Map Reads with BWA Element
  • Map Reads with BWA-MEM Element
  • Map Reads with UGENE Genome Aligner Element
  • Map RNA-Seq Reads with TopHat Element
• NGS: Metagenomics Classification
  • Build CLARK Database
  • Build DIAMOND Database
  • Build Kraken Database
  • Classification Report Element
  • Classify Sequences with CLARK
  • Classify Sequences with DIAMOND
  • Classify Sequences with Kraken
  • Classify Sequences with MetaPhlAn2
  • Ensemble Classification Data
  • Filter by Classification
  • Improve Classification with WEVOTE
• NGS: RNA-Seq Analysis
  • Assemble Transcripts with StringTie Element
  • Assembly Transcripts with Cufflinks Element
  • Extract Transcript Sequences with gffread Element
  • Merge Assemblies with Cuffmerge Element
  • StringTie Gene Abudance Report Element
  • Test for Diff. Expression with Cuffdiff Element
• NGS: Variant Analysis
  • Call Variants with SAMtools Element
  • Change Chromosome Notation for VCF Element
  • Convert SnpEff Variations to Annotations Element
  • Create VCF Consensus Element
  • SnpEff Annotation and Filtration Element
• Transcription Factor
  • Build Frequency Matrix Element
  • Build SITECON Model Element
  • Build Weight Matrix Element
  • Convert Frequency Matrix Element
  • Read Frequency Matrix Element
  • Read SITECON Model Element
  • Read Weight Matrix Element
  • Search for TFBS with SITECON Element
  • Search for TFBS with Weight Matrix Element
  • Write Frequency Matrix Element
  • Write SITECON Model Element
  • Write Weight Matrix Element
• Utils
  • DNA Statistics Element
  • Generate DNA Element