- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
---|---|---|---|
replace | https://w3id.org/cwl/view/git/26dad276bac124f89086268bcbca962a5c0caca6/utils/esl-reformat-replace.yaml#replace (Optional) | ||
blockSize | Float (Optional) | ||
buscoMode | https://w3id.org/cwl/view/git/26dad276bac124f89086268bcbca962a5c0caca6/tools/BUSCO/BUSCO-assessment_modes.yaml#assessment_modes | ||
i5Databases | Directory | ||
phmmerSeqdb | File [FASTA] | ||
buscoLineage | Directory | ||
clanInfoFile | File | ||
diamondSeqdb | File | ||
cmsearchCores | Integer | ||
i5Applications | https://w3id.org/cwl/view/git/26dad276bac124f89086268bcbca962a5c0caca6/tools/InterProScan/InterProScan-apps.yaml#apps[] (Optional) | ||
i5OutputFormat | https://w3id.org/cwl/view/git/26dad276bac124f89086268bcbca962a5c0caca6/tools/InterProScan/InterProScan-protein_formats.yaml#protein_formats[] (Optional) | ||
singleBestOnly | Boolean (Optional) | ||
buscoOutputName | String | ||
transcriptsFile | File [FASTA] | ||
covariance_models | File[] |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
identify_nc_rna |
cmsearch-multimodel-wf.cwl
(Workflow)
|
Identifies non-coding RNAs using Rfams covariance models | |
functional_analysis |
InterProScan-v5-chunked-wf.cwl
(Workflow)
|
Runs InterProScan on batches of sequences to retrieve functional annotations. | |
identify_coding_regions |
TransDecoder-v5-wf-2steps.cwl
(Workflow)
|
TransDecoder 2 step workflow, running TransDecoder.LongOrfs (step 1) followed by TransDecoder.Predict (step2) | |
calculate_phmmer_matches |
../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 https://github.com/EddyRivasLab/hmmer for full documentation. Releases can be downloaded from https://github.com/EddyRivasLab/hmmer/releases |
calculate_diamond_matches |
../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. |
run_transcriptome_assessment |
../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 http://busco.ezlab.org/ for full documentation. The BUSCO assessment software distribution is available from the public GitLab project: https://gitlab.com/ezlab/busco where it can be downloaded or cloned using a git client (git clone https://gitlab.com/ezlab/busco.git). 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. |
remove_asterisks_and_reformat |
../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 https://github.com/EddyRivasLab/easel |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
bed_output | File | ||
gff3_output | File | ||
i5Annotations | File | ||
coding_regions | File | ||
phmmer_matches | 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 | ||
busco_translated_proteins | Directory |
https://w3id.org/cwl/view/git/26dad276bac124f89086268bcbca962a5c0caca6/workflows/TranscriptsAnnotation-wf.cwl