Workflow: ACCESS_pipeline.cwl
Fetched 2024-09-22 12:21:14 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq1 | File[] | ||
| fastq2 | File[] | ||
| adapter | String[] | ||
| version | String | ||
| adapter2 | String[] | ||
| hotspots | File | ||
| add_rg_ID | String[] | ||
| add_rg_LB | Integer[] | ||
| add_rg_PU | String[] | ||
| add_rg_SM | String[] | ||
| gene_list | File | ||
| run_tools | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/collapsing_tools.yaml#run_tools | ||
| patient_id | String[] | ||
| title_file | File | ||
| inputs_yaml | File | ||
| abra__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/abra.yaml#abra__params | ||
| project_name | String | ||
| sample_class | String[] | ||
| sample_sheet | File[] | ||
| waltz__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/waltz.yaml#waltz__params | ||
| FP_config_file | File | ||
| fci_2__basq_fix | Boolean (Optional) | ||
| pool_a_bed_file | File | ||
| pool_b_bed_file | File | ||
| reference_fasta | String | ||
| trimgalore__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/trimgalore.yaml#trimgalore__params | ||
| print_reads__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/print_reads.yaml#print_reads__params | ||
| reference_fasta_fai | String | ||
| A_on_target_positions | File | ||
| B_on_target_positions | File | ||
| bqsr__knownSites_dbSNP | File | ||
| bqsr__knownSites_millis | File | ||
| mark_duplicates__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/mark_duplicates.yaml#mark_duplicates__params | ||
| noise__good_positions_A | File | ||
| base_recalibrator__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/base_recalibrator.yaml#base_recalibrator__params | ||
| pool_a_bed_file_exonlevel | File | ||
| marianas_collapsing__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/marianas_collapsing.yaml#marianas_collapsing__params | ||
| fix_mate_information__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/fix_mate_information.yaml#fix_mate_information__params | ||
| find_covered_intervals__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/find_covered_intervals.yaml#find_covered_intervals__params | ||
| process_loop_umi_fastq__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/process_loop_umi_fastq.yaml#process_loop_umi_fastq__params | ||
| add_or_replace_read_groups__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/add_or_replace_read_groups.yaml#add_or_replace_read_groups__params |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| standard_bam_generation |
standard_pipeline.cwl
(Workflow)
|
This is a workflow to go from UMI-tagged fastqs to standard bams. It does not include collapsing, or QC It does include modules 1 and 2 |
|
| standard_bam_to_collapsed_qc |
This is a workflow to go from standard bams to collapsed bams and QC results. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam_dirs | Directory[] | ||
| clstats1 | File[] | ||
| clstats2 | File[] | ||
| picard_qc | Directory | ||
| qc_tables | Directory | ||
| md_metrics | File[] | ||
| combined_qc | Directory | ||
| duplex_bams | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/bam_sample.yaml#bam_sample[] | ||
| simplex_bams | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/bam_sample.yaml#bam_sample[] | ||
| clipping_info | File[] | ||
| standard_bams | File[] | ||
| fci_covint_bed | File[] | ||
| fci_covint_list | File[] | ||
| unfiltered_bams | File[] | ||
| hotspots_in_normals_data | File | ||
| recalibrated_scores_matrix | addbaa0ce100d540fd7bda610c0de925[] |
Permalink:
https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/workflows/ACCESS_pipeline.cwl
