workflows

Examples of CWL workflows using EBI Web Services and Sample Clients

Examples of CWL workflows chaining multiple tools together.

Running CWL for EBI tools (requires local copy of the clients)

Note: Before running cwltool, you may want to edit the values for the parameters, including adding a required email address. Running these CWL files expects webservice-clients directory to be found alongside the webservice-cwl directory.

Run NCBI BLAST+, Dbfetch, Clustal Omega and then Simple Phylogeny

Input string sequence -> blast search, output: ids -> dbfetch, output: protein sequences -> clustal omega, output: Multiple sequence alignment -> simple phylogeny, output: phylogeny tree

Explore this workflow with CWL viewer or test it yourself:

cwltool workflow-blast-clustalo-phylogeny.cwl inputs-blast-clustalo-phylogeny.yml

Run NCBI BLAST+, EBI Search (a.k.a. ebeye) and PDBe (API)

Input sequence string -> blast search, output: ids -> EBI search, output: structural homologs to original sequence -> PDBe API, output: summary information about the structure

Explore this workflow with CWL viewer or test it yourself:

cwltool workflow-blast-ebeye-pdbe.cwl inputs-blast-ebeye-pdbe.yml

Run NCBI BLAST+ and Phobius

Input sequence string -> blast search, output: protein sequence -> phobius, output: protein topology

Explore this workflow with CWL viewer or test it yourself:

cwltool workflow-blast-phobius.cwl inputs-blast-phobius.yml

Run Dbfetch and Phobius

Input sequence string -> fetch search, output: protein sequence -> phobius, output: protein topology

Explore this workflow with CWL viewer or test it yourself:

cwltool workflow-fetch-phobius.cwl inputs-fetch-phobius.yml

Run EMBOSS transeq, NCBI BLAST+, InterProScan5 and Clustal Omega

Unknown DNA sequence file -> emboss_transeq, output: translated protein sequence -> blast search, output: ids -> dbfetch, output: protein sequences -> clustal omega, output: Multiple sequence alignment -> simple phylogeny, output: phylogeny tree Additional output: translated protein sequence -> iprscan5, output: out file

Explore this workflow with CWL viewer or test it yourself:

cwltool workflow-transeq-blast-clustalo.cwl inputs-transeq-blast-clustalo.yml

Run FASTA and Pratt

Input protein sequence file -> fasta, output: ids -> dbfetch, output: protein sequence -> pratt, output: patterns in unaligned sequences

Explore this workflow with CWL viewer or test it yourself:

cwltool workflow-fasta-pratt.cwl inputs-fasta-pratt.yml

Run Dbfetch and HMMER3 hmmscan

Input sequence string -> dbfetch, output: protein sequence -> hmmer3_hmmscan, output: ids

Explore this workflow with CWL viewer or test it yourself:

cwltool workflow-fetch-hmmscan.cwl inputs-fetch-hmmscan.yml

Run EMBOSS pepinfo, backtranseq and cpgplot

Input protein sequence file -> emboss_backtranseq, output: corresponding DNA sequence -> emboss_cpgplot, output: cpg island plot Additional output: protein sequence -> emboss_pepinfo, output: amino acid properties

Explore this workflow with CWL viewer or test it yourself:

cwltool workflow-pepinfo-backtranseq-cpgplot.cwl inputs-pepinfo-backtranseq-cpgplot.yml

Run HMMER3 phmmer and NCBI BLAST+

Input protein sequence file -> hmmer3_phmmer, output: ids -> dbfetch, output: protein sequence -> blast (multifasta to search all sequences), output: ids

Explore this workflow with CWL viewer or test it yourself:

cwltool workflow-phmmer-blast.cwl inputs-phmmer-blast.yml

Run EBI Search for Taxonomy IDs

Input protein name query -> ebisearch [Perl client], output: taxonomy ids
Input protein name query -> ebisearch [API], output: taxonomy ids

Explore this workflow with CWL viewer or test it yourself:

cwltool workflow-ebisearch.cwl inputs-ebisearch.yml