Workflow: Chunked version of phmmer-v3.2.cwl
Fetched 2024-05-17 23:24:33 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| cpu | Integer (Optional) | Number of parallel CPU workers to use for multithreads | |
| seqdb | File | Target database of sequences | |
| seqFile | File | Query sequence(s) file |
Search one or more query protein sequences against a protein sequence database. |
| fullPhmmerOutput | String | ||
| bitscoreThreshold | Integer (Optional) | report sequences >= this bit score threshold in output | |
| fullPhmmerMatches | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| split_seqs |
../utils/fasta_chunker.cwl
(CommandLineTool)
|
split FASTA by number of records |
based upon code by developers from EMBL-EBI |
| combine_phmmer_output |
../utils/concatenate.cwl
(CommandLineTool)
|
Redirecting Multiple Files Contain in a Single File |
The cat (short for “concatenate“) command is one of the most frequently used command in Linux/Unix like operating systems. cat command allows us to create single or multiple files, view contain of file, concatenate files and redirect output in terminal or files. |
| combine_phmmer_matches |
../utils/concatenate.cwl
(CommandLineTool)
|
Redirecting Multiple Files Contain in a Single File |
The cat (short for “concatenate“) command is one of the most frequently used command in Linux/Unix like operating systems. cat command allows us to create single or multiple files, view contain of file, concatenate files and redirect output in terminal or files. |
| 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 |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| matches | File | ||
| programOutput | File |
https://w3id.org/cwl/view/git/e9bbe2917384efc75ba067db23612bc8e22f3f06/workflows/phmmer-v3.2-chunked-wf.cwl
