Workflow: qc-basic.workflow.cwl
Fetched 2023-01-12 22:35:45 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 2-clause "Simplified" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| jobid | String | ||
| sequences | File | ||
| kmerLength | Integer[] (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| kmer |
../Tools/kmer-tool.tool.cwl
(CommandLineTool)
|
calcualate kmer bins |
Script to use jellyfish to get kmer information Input:\ fasta/fastq file Output:\ kmer information, one of:\ 1. hash:\ binary hash of counts 2. stats:\ summary stats 3. dump:\ profile (kmer seq - count) 4. histo:\ histogram (count - abundance) 5. histo ranked:\ count, abundance, count*abundance, reverse-sum(abundance), reverse-sum(count*abundance), ratio-to-largest |
| drisee |
../Tools/drisee.tool.cwl
(CommandLineTool)
|
||
| consensus |
../Tools/consensus.tool.cwl
(CommandLineTool)
|
||
| formatQcStats |
../Tools/format_qc_stats.tool.cwl
(CommandLineTool)
|
||
| sequenceStats |
../Tools/seq_length_stats.tool.cwl
(CommandLineTool)
|
sequence statistics |
Calculate statistics for fasta files. Output fields:\ bp_count sequence_count average_length standard_deviation_length length_min length_max average_gc_content standard_deviation_gc_content average_gc_ratio standard_deviation_gc_ratio ambig_char_count ambig_sequence_count average_ambig_chars sequence_type |
| formatSequenceStats |
../Tools/format_seq_stats.tool.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| qcStatFile | File | ||
| seqBinFile | File | ||
| seqStatFile | File | ||
| qcSummaryFile | File |
Permalink:
https://w3id.org/cwl/view/git/f906212e2c9a88280ae36545e5422f25752aa8f4/CWL/Workflows/qc-basic.workflow.cwl
