Workflow: get_spike_in_counts.cwl
Fetched 2024-05-10 06:41:00 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- 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 |
|---|---|---|---|
| sample_id | String | ||
| is_paired_end | Boolean | ||
| fastq1_trimmed | File[] | ||
| fastq2_trimmed | File[] | ||
| genome_spike_in | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| mapping |
../tools/bowtie2.cwl
(CommandLineTool)
|
||
| sam2bam |
../tools/samtools_view_sam2bam.cwl
(CommandLineTool)
|
||
| sort_bam |
../tools/samtools_sort.cwl
(CommandLineTool)
|
Sort a bam file by read names. |
|
| duplicate_removal |
../tools/picard_markdup.cwl
(CommandLineTool)
|
||
| count_aligned_reads |
../tools/samtools_view_count_alignments.cwl
(CommandLineTool)
|
||
| lane_replicate_merging |
../tools/samtools_merge.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File | ||
| aln_read_count | Long | ||
| aln_read_count_file | File |
Permalink:
https://w3id.org/cwl/view/git/8526687739a6802eeb08e97b27c20010225d5eb5/CWL/workflow_modules/get_spike_in_counts.cwl
