Workflow: transform.cwl
Fetched 2023-01-04 03:43:18 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 |
|---|---|---|---|
| bam_name | String | ||
| job_uuid | String | ||
| known_snp | File | ||
| run_bamindex | Long[] | ||
| thread_count | Long | ||
| reference_sequence | File | ||
| run_markduplicates | Long[] | ||
| common_biallelic_vcf | File | ||
| readgroups_bam_file_list | https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/tools/readgroup.yml#readgroups_bam_file[] | ||
| capture_kit_set_file_list | https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/tools/capture_kit.yml#capture_kit_set_file[] | ||
| amplicon_kit_set_file_list | https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/tools/amplicon_kit.yml#amplicon_kit_set_file[] | ||
| readgroup_fastq_pe_file_list | https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/tools/readgroup.yml#readgroup_fastq_pe_file[] | ||
| readgroup_fastq_se_file_list | https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/tools/readgroup.yml#readgroup_fastq_se_file[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bwa_o1 |
bwa_se.cwl
(Workflow)
|
||
| bwa_o2 |
bwa_se.cwl
(Workflow)
|
||
| bwa_pe |
bwa_pe.cwl
(Workflow)
|
||
| bwa_se |
bwa_se.cwl
(Workflow)
|
||
| metrics |
metrics.cwl
(Workflow)
|
||
| integrity |
integrity.cwl
(Workflow)
|
||
| bam_reheader |
../../tools/bam_reheader.cwl
(CommandLineTool)
|
||
| fastq_clean_pe |
fastq_clean_pe.cwl
(Workflow)
|
||
| fastq_clean_se |
fastq_clean_se.cwl
(Workflow)
|
||
| gatk_applybqsr |
../../tools/gatk4_applybqsr.cwl
(CommandLineTool)
|
||
| merge_all_sqlite |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| conditional_index |
conditional_bamindex.cwl
(Workflow)
|
||
| merge_sqlite_bwa_pe |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| merge_sqlite_bwa_se |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| picard_mergesamfiles |
../../tools/picard_mergesamfiles_aoa.cwl
(CommandLineTool)
|
||
| gatk_baserecalibrator |
../../tools/gatk4_baserecalibrator.cwl
(CommandLineTool)
|
||
| merge_o1_fastq_records |
../../tools/merge_se_fastq_records.cwl
(ExpressionTool)
|
||
| merge_o2_fastq_records |
../../tools/merge_se_fastq_records.cwl
(ExpressionTool)
|
||
| merge_pe_fastq_records |
../../tools/merge_pe_fastq_records.cwl
(ExpressionTool)
|
||
| merge_se_fastq_records |
../../tools/merge_se_fastq_records.cwl
(ExpressionTool)
|
||
| conditional_markduplicates |
conditional_markduplicates.cwl
(Workflow)
|
||
| merge_bam_pe_fastq_records |
../../tools/merge_pe_fastq_records.cwl
(ExpressionTool)
|
||
| merge_bam_se_fastq_records |
../../tools/merge_se_fastq_records.cwl
(ExpressionTool)
|
||
| decide_markduplicates_index |
../../tools/decider_conditional_bams.cwl
(ExpressionTool)
|
||
| merge_sqlite_fastq_clean_pe |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| merge_sqlite_fastq_clean_se |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| picard_validatesamfile_bqsr |
../../tools/picard_validatesamfile.cwl
(CommandLineTool)
|
||
| picard_validatesamfile_bqsr_to_sqlite |
../../tools/picard_validatesamfile_to_sqlite.cwl
(CommandLineTool)
|
||
| readgroups_bam_to_readgroups_fastq_lists |
readgroups_bam_to_readgroups_fastq_lists.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| sqlite | File | ||
| output_bam | File |
Permalink:
https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/workflows/bamfastq_align/transform.cwl
