- 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[] | ||
readgroups_bam_file_list | https://w3id.org/cwl/view/git/f34d3963b33e0a379338cb3cb75b0016f012bf2c/tools/readgroup.yml#readgroups_bam_file[] | ||
capture_kit_set_file_list | https://w3id.org/cwl/view/git/f34d3963b33e0a379338cb3cb75b0016f012bf2c/tools/capture_kit.yml#capture_kit_set_file[] | ||
amplicon_kit_set_file_list | https://w3id.org/cwl/view/git/f34d3963b33e0a379338cb3cb75b0016f012bf2c/tools/amplicon_kit.yml#amplicon_kit_set_file[] | ||
readgroup_fastq_pe_file_list | https://w3id.org/cwl/view/git/f34d3963b33e0a379338cb3cb75b0016f012bf2c/tools/readgroup.yml#readgroup_fastq_pe_file[] | ||
readgroup_fastq_se_file_list | https://w3id.org/cwl/view/git/f34d3963b33e0a379338cb3cb75b0016f012bf2c/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)
|
||
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)
|
||
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/f34d3963b33e0a379338cb3cb75b0016f012bf2c/workflows/bamfastq_align/transform.cwl