Workflow: preprocess-ont.cwl
Fetched 2023-01-11 15:39:53 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| ref_human_genome | File | ||
| illumina_accession | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastqc |
../bio-cwl-tools/fastqc/fastqc_2.cwl
(CommandLineTool)
|
Tool runs FastQC from Babraham Bioinformatics |
|
| multiqc |
../bio-cwl-tools/multiqc/multiqc.cwl
(CommandLineTool)
|
Run multiqc on log files from supported bioinformatic tools. 26/04/2020: Fixed output filenames, added support for a single input file in qc_files_array (Miguel Boland) |
|
| sam2bam |
../bio-cwl-tools/samtools/samtools_view_sam2bam.cwl
(CommandLineTool)
|
Convert SAM to BAM. |
|
| minimap2 |
../bio-cwl-tools/minimap2/minimap2.cwl
(CommandLineTool)
|
This CWL file defines running minimap2 to align some sequences to a database. We assume the database has been indexed. This is not necessary but we will do it in our use case |
|
| nanoplot |
../bio-cwl-tools/nanoplot/nanoplot.cwl
(CommandLineTool)
|
||
| rename_bam |
../bio-cwl-tools/util/rename.cwl
(ExpressionTool)
|
Also consider https://www.commonwl.org/user_guide/misc/#rename-an-input-file or https://www.commonwl.org/user_guide/misc/#rename-an-output-file |
|
| fetch_fastqs |
Worfklow combining an SRA fetch from NCBI with a fastq-dump cmd |
||
| rename_fastq |
../bio-cwl-tools/util/rename.cwl
(ExpressionTool)
|
Also consider https://www.commonwl.org/user_guide/misc/#rename-an-input-file or https://www.commonwl.org/user_guide/misc/#rename-an-output-file |
|
| samtools_fastq |
../bio-cwl-tools/samtools/samtools_fastq.cwl
(CommandLineTool)
|
Bam to fastq conversion |
|
| rename_fastqc_zip |
../bio-cwl-tools/util/rename.cwl
(ExpressionTool)
|
Also consider https://www.commonwl.org/user_guide/misc/#rename-an-input-file or https://www.commonwl.org/user_guide/misc/#rename-an-output-file |
|
| rename_multiqc_zip |
../bio-cwl-tools/util/rename.cwl
(ExpressionTool)
|
Also consider https://www.commonwl.org/user_guide/misc/#rename-an-input-file or https://www.commonwl.org/user_guide/misc/#rename-an-output-file |
|
| rename_multiqc_html |
../bio-cwl-tools/util/rename.cwl
(ExpressionTool)
|
Also consider https://www.commonwl.org/user_guide/misc/#rename-an-input-file or https://www.commonwl.org/user_guide/misc/#rename-an-output-file |
|
| rename_fastqc_summary |
../bio-cwl-tools/util/rename.cwl
(ExpressionTool)
|
Also consider https://www.commonwl.org/user_guide/misc/#rename-an-input-file or https://www.commonwl.org/user_guide/misc/#rename-an-output-file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File | ||
| fastqc_zip | File | ||
| multiqc_zip | File | ||
| multiqc_html | File | ||
| fastqc_summary | File | ||
| original_fastq1 | File |
https://w3id.org/cwl/view/git/2f7764f063e198fd8601229105922f913ea89941/PreProcessing/preprocess-ont.cwl
