Workflow: transform.cwl
Fetched 2023-01-05 02:02:45 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 |
|---|---|---|---|
| job_uuid | String | ||
| input_bam | File | ||
| known_snp | File | ||
| thread_count | Long | ||
| reference_sequence | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bwa_o1 |
../../tools/bwa_se.cwl
(CommandLineTool)
|
||
| bwa_o2 |
../../tools/bwa_se.cwl
(CommandLineTool)
|
||
| bwa_pe |
../../tools/bwa_pe.cwl
(CommandLineTool)
|
||
| bwa_se |
../../tools/bwa_se.cwl
(CommandLineTool)
|
||
| fastqc1 |
../../tools/fastqc.cwl
(CommandLineTool)
|
||
| fastqc2 |
../../tools/fastqc.cwl
(CommandLineTool)
|
||
| fastqc_s |
../../tools/fastqc.cwl
(CommandLineTool)
|
||
| fastqc_o1 |
../../tools/fastqc.cwl
(CommandLineTool)
|
||
| fastqc_o2 |
../../tools/fastqc.cwl
(CommandLineTool)
|
||
| integrity |
integrity.cwl
(Workflow)
|
||
| fastqc_db1 |
../../tools/fastqc_db.cwl
(CommandLineTool)
|
||
| fastqc_db2 |
../../tools/fastqc_db.cwl
(CommandLineTool)
|
||
| fastqc_db_s |
../../tools/fastqc_db.cwl
(CommandLineTool)
|
||
| bam_reheader |
../../tools/bam_reheader.cwl
(CommandLineTool)
|
||
| fastqc_db_o1 |
../../tools/fastqc_db.cwl
(CommandLineTool)
|
||
| fastqc_db_o2 |
../../tools/fastqc_db.cwl
(CommandLineTool)
|
||
| metrics_bqsr |
mixed_library_metrics.cwl
(Workflow)
|
||
| decider_bwa_o1 |
../../tools/decider_bwa_expression.cwl
(ExpressionTool)
|
||
| decider_bwa_o2 |
../../tools/decider_bwa_expression.cwl
(ExpressionTool)
|
||
| decider_bwa_pe |
../../tools/decider_bwa_expression.cwl
(ExpressionTool)
|
||
| decider_bwa_se |
../../tools/decider_bwa_expression.cwl
(ExpressionTool)
|
||
| gatk_applybqsr |
../../tools/gatk4_applybqsr.cwl
(CommandLineTool)
|
||
| merge_all_sqlite |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| picard_sortsam_o1 |
../../tools/picard_sortsam.cwl
(CommandLineTool)
|
||
| picard_sortsam_o2 |
../../tools/picard_sortsam.cwl
(CommandLineTool)
|
||
| picard_sortsam_pe |
../../tools/picard_sortsam.cwl
(CommandLineTool)
|
||
| picard_sortsam_se |
../../tools/picard_sortsam.cwl
(CommandLineTool)
|
||
| readgroup_json_db |
../../tools/readgroup_json_db.cwl
(CommandLineTool)
|
||
| samtools_bamtobam |
../../tools/samtools_bamtobam.cwl
(CommandLineTool)
|
||
| biobambam_bamtofastq |
../../tools/biobambam2_bamtofastq.cwl
(CommandLineTool)
|
||
| picard_mergesamfiles |
../../tools/picard_mergesamfiles.cwl
(CommandLineTool)
|
||
| bam_readgroup_to_json |
../../tools/bam_readgroup_to_json.cwl
(CommandLineTool)
|
||
| gatk_baserecalibrator |
../../tools/gatk4_baserecalibrator.cwl
(CommandLineTool)
|
||
| picard_markduplicates |
../../tools/picard_markduplicates.cwl
(CommandLineTool)
|
||
| sort_scattered_fastq1 |
../../tools/sort_scatter_expression.cwl
(ExpressionTool)
|
||
| sort_scattered_fastq2 |
../../tools/sort_scatter_expression.cwl
(ExpressionTool)
|
||
| sort_scattered_fastq_s |
../../tools/sort_scatter_expression.cwl
(ExpressionTool)
|
||
| merge_fastqc_db1_sqlite |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| merge_fastqc_db2_sqlite |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| merge_readgroup_json_db |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| picard_mergesamfiles_o1 |
../../tools/picard_mergesamfiles.cwl
(CommandLineTool)
|
||
| picard_mergesamfiles_o2 |
../../tools/picard_mergesamfiles.cwl
(CommandLineTool)
|
||
| picard_mergesamfiles_pe |
../../tools/picard_mergesamfiles.cwl
(CommandLineTool)
|
||
| picard_mergesamfiles_se |
../../tools/picard_mergesamfiles.cwl
(CommandLineTool)
|
||
| remove_duplicate_fastq1 |
../../tools/fastq_remove_duplicate_qname.cwl
(CommandLineTool)
|
||
| remove_duplicate_fastq2 |
../../tools/fastq_remove_duplicate_qname.cwl
(CommandLineTool)
|
||
| sort_scattered_fastq_o1 |
../../tools/sort_scatter_expression.cwl
(ExpressionTool)
|
||
| sort_scattered_fastq_o2 |
../../tools/sort_scatter_expression.cwl
(ExpressionTool)
|
||
| merge_fastqc_db_s_sqlite |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| remove_duplicate_fastq_s |
../../tools/fastq_remove_duplicate_qname.cwl
(CommandLineTool)
|
||
| fastqc_o1_basicstats_json |
../../tools/fastqc_basicstatistics_json.cwl
(CommandLineTool)
|
||
| fastqc_o2_basicstats_json |
../../tools/fastqc_basicstatistics_json.cwl
(CommandLineTool)
|
||
| fastqc_pe_basicstats_json |
../../tools/fastqc_basicstatistics_json.cwl
(CommandLineTool)
|
||
| fastqc_se_basicstats_json |
../../tools/fastqc_basicstatistics_json.cwl
(CommandLineTool)
|
||
| merge_fastqc_db_o1_sqlite |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| merge_fastqc_db_o2_sqlite |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| remove_duplicate_fastq_o1 |
../../tools/fastq_remove_duplicate_qname.cwl
(CommandLineTool)
|
||
| remove_duplicate_fastq_o2 |
../../tools/fastq_remove_duplicate_qname.cwl
(CommandLineTool)
|
||
| picard_validatesamfile_bqsr |
../../tools/picard_validatesamfile.cwl
(CommandLineTool)
|
||
| picard_markduplicates_to_sqlite |
../../tools/picard_markduplicates_to_sqlite.cwl
(CommandLineTool)
|
||
| picard_validatesamfile_original |
../../tools/picard_validatesamfile.cwl
(CommandLineTool)
|
||
| picard_validatesamfile_bqsr_to_sqlite |
../../tools/picard_validatesamfile_to_sqlite.cwl
(CommandLineTool)
|
||
| picard_validatesamfile_original_to_sqlite |
../../tools/picard_validatesamfile_to_sqlite.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File | ||
| sqlite | File |
Permalink:
https://w3id.org/cwl/view/git/a3eec6c1081d28efe00a0d269fb41303acc4ccdd/workflows/dnaseq/transform.cwl
