Workflow: preprocess-illumina.cwl
Fetched 2024-11-23 20:13:01 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| hg38 | File | ||
| illumina_accession | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastp |
../bio-cwl-tools/fastp/fastp.cwl
(CommandLineTool)
|
Modified from https://github.com/nigyta/bact_genome/blob/master/cwl/tool/fastp/fastp.cwl |
|
| bwa_mem |
../bio-cwl-tools/bwa/BWA-Mem.cwl
(CommandLineTool)
|
||
| 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) |
|
| 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 |
||
| samtools_view |
../bio-cwl-tools/samtools/samtools_view_sam2bam.cwl
(CommandLineTool)
|
Convert SAM to BAM. |
|
| samtools_fastq |
../bio-cwl-tools/samtools/samtools_fastq.cwl
(CommandLineTool)
|
Bam to fastq conversion |
|
| rename_fastp_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_fastp_json |
../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 |
|
| unpack_ref_genome |
tools/unpack_ref_db.cwl
(CommandLineTool)
|
decompression tool using Lempel-Ziv coding (LZ77) |
|
| 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 |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File [BAM] | ||
| multiqc_zip | File [JSON] | ||
| mapped_fastq | File [FASTQ] | ||
| multiqc_html | File [HTML] | ||
| original_fastq1 | File [FASTQ] | ||
| original_fastq2 | File (Optional) [FASTQ] | ||
| fastp_html_report | File [HTML] | ||
| fastp_json_report | File [JSON] |
https://w3id.org/cwl/view/git/3114ddd28bbee5505a9819b1a84f4896fd0b0992/PreProcessing/preprocess-illumina.cwl
