Workflow: samples_fillout_index_batch_workflow.cwl
Fetched 2025-02-14 20:25:11 GMT
Verified with cwltool version 3.1.20230201224320
Wrapper to run bam indexing on all bams before submitting for samples fillout Also includes steps to pre-filter some maf input files NOTE: each sample in a sample_group must have a .bam file, and there must be a minumum of 1 .maf file amoungst samples in the same sample_group this means that for each sample in the sample_group, a .bam is required but a .maf is optional as long as one sample in the group has a .maf this also means that singleton sample groups, or a sample group with only one sample, MUST include a .maf file; singletons cannot lack a .maf NOTE: all .maf files must be valid, at a minimum they must have a header and at least one variant if a sample has no variants in its .maf file, or has an empty .maf file, then it should NOT have a maf_file entry associated with it
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| is_impact | Boolean | ||
| ref_fasta | File | ||
| exac_filter | File | ||
| sample_groups | 15769cf8f3aa54ff207ada14d113b772[] |
a nested list of lists of grouped samples |
|
| argos_version_string | String (Optional) | ||
| fillout_output_fname | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| concat_portal_file |
concat-tables.cwl
(CommandLineTool)
|
||
| concat_output_files |
concat-tables.cwl
(CommandLineTool)
|
||
| concat_filtered_file |
concat-tables.cwl
(CommandLineTool)
|
||
| concat_uncalled_file |
concat-tables.cwl
(CommandLineTool)
|
||
| concat_singleton_files |
samples_fillout_index_batch_workflow.cwl#concat_singleton_files/run/concat_singleton_files
(CommandLineTool)
|
concat_singleton_files | |
| split_singleton_groups |
8476569528ba46aa49e1b10e8c69a8c3
(ExpressionTool)
|
||
| run_samples_fillout_index_workflow | run_samples_fillout_index_workflow |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File | ||
| portal_file | File | ||
| filtered_file | File | ||
| uncalled_file | File |
https://w3id.org/cwl/view/git/462f6015c9268a4205b6e81de018a470b8a4a153/cwl/samples_fillout_index_batch_workflow.cwl
