- 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/4e4d2e674bde612f98f2b0370445f8b2a47587df/CWL/Workflows/qc-basic.workflow.cwl