Workflow: map medium and long reads (greater than 100 bp) against reference genome
Fetched 2024-11-27 10:40:53 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
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- Default Values
- Nested Workflows
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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 |
|---|---|---|---|
| sort_mode | How to sort the alignments, if at all |
* coordinate: Sort by chromosomal coordinates * name: Sort by read names (i.e., the QNAME field) * unsorted: Not sorted (sorted as input) |
|
| read_group | https://w3id.org/cwl/view/git/1bfe9fc07978c8463399eec690798effb8431c35/bwa/ReadGroupType.yml#ReadGroupDetails (Optional) | Specify read group details manually. | |
| do_auto_name | Boolean | Auto-assign read groups |
If true, use the file name to automatically assign the read groups value. |
| paired_reads_1 | File [FASTQ-sanger] | First (forward) set of the paired reads | |
| paired_reads_2 | File [FASTQ-sanger] | Second (reverse) set of the paired reads | |
| reference_genome | File [FASTA] | Reference genome sequences, optionally already indexed for BWA-Mem2. |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort |
../samtools/samtools_sort.cwl
(CommandLineTool)
|
Sort a bam file by read names. |
|
| align |
BWA-Mem2.cwl
(CommandLineTool)
|
map medium and long reads (> 100 bp) against reference genome | |
| index_genome |
BWA-Mem2-index.cwl
(CommandLineTool)
|
||
| compute_read_group_header |
ReadGroup.cwl
(ExpressionTool)
|
||
| convert_unsorted_alignments_to_bam |
../samtools/samtools_view_sam2bam.cwl
(CommandLineTool)
|
Convert SAM to BAM. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| alignments | File [BAM] | Alignments of the reads to the references genome |
Permalink:
https://w3id.org/cwl/view/git/1bfe9fc07978c8463399eec690798effb8431c35/bwa/BWA-Mem2-paired.cwl
