Workflow: Transcripts annotation workflow

Fetched 2023-01-12 19:42:19 GMT
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ID Type Title Doc
replace (Optional)
blockSize Float (Optional)
i5Databases Directory
buscoLineage Directory
clanInfoFile File
diamondSeqdb File
cmsearchCores Integer
i5_chunk_size Integer (Optional)
i5Applications[] (Optional)
i5OutputFormat[] (Optional)
singleBestOnly Boolean (Optional)
buscoOutputName String
transcriptsFile File [FASTA]
covariance_models File[]


ID Runs Label Doc
identify_nc_rna Identifies non-coding RNAs using Rfams covariance models
../utils/cut_fasta_headers.cwl (CommandLineTool)
Cuts FASTA headers which are too long

Cuts away everything after the first whitespace character.

../utils/clean_fasta_headers.cwl (CommandLineTool)
Replaces problematic characters from FASTA headers with dashes
functional_analysis Runs InterProScan on batches of sequences to retrieve functional annotations.
identify_coding_regions TransDecoder 2 step workflow, running TransDecoder.LongOrfs (step 1) followed by TransDecoder.Predict (step2)
../tools/Diamond/Diamon.blastx-v0.9.21.cwl (CommandLineTool)
Aligns DNA query sequences against a protein reference database

DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

The key features are: + Pairwise alignment of proteins and translated DNA at 500x-20,000x speed of BLAST. + Frameshift alignments for long read analysis. + Low resource requirements and suitable for running on standard desktops or laptops. + Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.

Please visit for full documentation.

Releases can be downloaded from

../tools/BUSCO/BUSCO-v3.cwl (CommandLineTool)
Assesses genome assembly and annotation completeness with single-copy orthologs

BUSCO v3 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9. BUSCO assessments are implemented in open-source software, with a large selection of lineage-specific sets of Benchmarking Universal Single-Copy Orthologs. These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines. Please visit for full documentation. The BUSCO assessment software distribution is available from the public GitLab project: where it can be downloaded or cloned using a git client (git clone We encourage users to opt for the git client option in order to facilitate future updates. BUSCO is written for Python 3.x and Python 2.7+. It runs with the standard packages. We recommend using Python3 when available.

../utils/esl-reformat.cwl (CommandLineTool)
Normalizes input sequences to FASTA using esl-reformat

Normalizes input sequences to FASTA with fixed number of sequence characters per line using esl-reformat from


ID Type Label Doc
bed_output File
gff3_output File
i5Annotations File
coding_regions File
diamond_matches File
busco_full_table File
peptide_sequences File
busco_blast_output Directory
busco_hmmer_output Directory
busco_short_summary File
busco_missing_buscos File
deoverlapped_matches File
reformatted_sequences File
cutted_transcripts_file File [FASTA]
cleaned_transcripts_file File [FASTA]
busco_translated_proteins Directory