Workflow: animal-genome-assembly.cwl
Fetched 2023-01-09 15:07:49 GMT
Verified with cwltool version 3.1.20221201130942
Animal Genome Assembly pipeline by Kazuharu Arakawa (@gaou_ak) without assembly step by canu, CWLized by Tazro Ohta (@inutano)
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- |
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| THREADS | Integer | ||
| INPUT_LONGREAD | File | ||
| INPUT_SHORTREAD | File | ||
| ESTIMATED_GENOME_SIZE | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| wtdbg2 |
../../tool/wtdbg2/wtdbg2/wtdbg2.cwl
(CommandLineTool)
|
string |
|
| nanoplot |
../../tool/nanoplot/nanoplot.cwl
(CommandLineTool)
|
string |
|
| wtpoa-cns |
../../tool/wtdbg2/wtpoa-cns/wtpoa-cns.cwl
(CommandLineTool)
|
string |
|
| jellyfish-count |
../../tool/jellyfish/count/jellyfish-count.cwl
(CommandLineTool)
|
string |
|
| jellyfish-histo |
../../tool/jellyfish/histo/jellyfish-histo.cwl
(CommandLineTool)
|
string |
|
| error_correction1 |
hybrid_error_correction.cwl
(Workflow)
|
Sub workflow used in the Animal Genome Assembly pipeline by Kazuharu Arakawa (@gaou_ak), CWLized by Tazro Ohta (@inutano) |
|
| error_correction2 |
hybrid_error_correction.cwl
(Workflow)
|
Sub workflow used in the Animal Genome Assembly pipeline by Kazuharu Arakawa (@gaou_ak), CWLized by Tazro Ohta (@inutano) |
|
| error_correction3 |
hybrid_error_correction.cwl
(Workflow)
|
Sub workflow used in the Animal Genome Assembly pipeline by Kazuharu Arakawa (@gaou_ak), CWLized by Tazro Ohta (@inutano) |
|
| error_correction4 |
hybrid_error_correction.cwl
(Workflow)
|
Sub workflow used in the Animal Genome Assembly pipeline by Kazuharu Arakawa (@gaou_ak), CWLized by Tazro Ohta (@inutano) |
|
| bbmap-stats-initial |
../../tool/bbmap/bbmap-stats/bbmap-stats.cwl
(CommandLineTool)
|
Output statistics of input sequence reads |
|
| bbmap-stats-wtdbg2-contigs |
../../tool/bbmap/bbmap-stats/bbmap-stats.cwl
(CommandLineTool)
|
Output statistics of input sequence reads |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| nanoplot_NanoStats | File | ||
| wtpoa-cns_output_file | File | ||
| jellyfish-histo_stdout | File | ||
| error_corrected_fasta_1 | File | ||
| error_corrected_fasta_2 | File | ||
| error_corrected_fasta_3 | File | ||
| error_corrected_fasta_4 | File | ||
| nanoplot_NanoPlot-report | File | ||
| nanoplot_Yield_By_Length | File | ||
| bbmap-stats-initial_stats | File | ||
| nanoplot_HistogramReadlength | File | ||
| bbmap-stats-wtdbg2-contigs_stats | File | ||
| nanoplot_Weighted_HistogramReadlength | File | ||
| nanoplot_LengthvsQualityScatterPlot_dot | File | ||
| nanoplot_LengthvsQualityScatterPlot_kde | File | ||
| nanoplot_LogTransformed_HistogramReadlength | File | ||
| nanoplot_Weighted_LogTransformed_HistogramReadlength | File |
Permalink:
https://w3id.org/cwl/view/git/b63171820f546def8c26f558182912a71af88b48/workflow/animal-genome-assembly/animal-genome-assembly.cwl
