Workflow: Transcripts annotation workflow

Fetched 2021-01-12 22:44:47 GMT
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ID Type Title Doc
i5Databases Directory
singleBestOnly Boolean (Optional)
replace (Optional)
i5OutputFormat[] (Optional)
buscoOutputName String
blockSize Float (Optional)
i5Applications[] (Optional)
diamondSeqdb File
clanInfoFile File
cmsearchCores Integer
transcriptsFile File [FASTA]
covariance_models File[]
buscoLineage Directory
phmmerSeqdb File [FASTA]


ID Runs Label Doc
identify_nc_rna Identifies non-coding RNAs using Rfams covariance models
../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

../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

identify_coding_regions TransDecoder 2 step workflow, running TransDecoder.LongOrfs (step 1) followed by TransDecoder.Predict (step2)
../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.

../tools/HMMER/phmmer-v3.2.cwl (CommandLineTool)
Search a single protein sequence against a protein sequence database. (BLASTP-like)

The phmmer and jackhmmer programs search a single protein sequence against a protein sequence database, akin to BLASTP and PSIBLAST, respectively. (Internally, they just produce a profile HMM from the query sequence, then run HMM searches.) Please visit for full documentation. Releases can be downloaded from

functional_analysis Runs InterProScan on batches of sequences to retrieve functional annotations.


ID Type Label Doc
coding_regions File
deoverlapped_matches File
busco_hmmer_output Directory
busco_translated_proteins Directory
i5Annotations File
busco_blast_output Directory
busco_missing_buscos File
bed_output File
peptide_sequences File
reformatted_sequences File
busco_full_table File
busco_short_summary File
gff3_output File
phmmer_matches File
diamond_matches File