Workflow: Replace legacy AML Trio Assay
Fetched 2025-12-13 21:22:33 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 |
|---|---|---|---|
| docm_vcf | File |
Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY) |
|
| omni_vcf | File | ||
| vep_pick | |||
| intervals | 15653dac1c6b8e25cc329fb0132f9111[] | ||
| reference | String | ||
| tumor_name | String (Optional) | ||
| normal_name | String (Optional) | ||
| somalier_vcf | File | ||
| followup_name | String (Optional) | ||
| gvcf_gq_bands | String[] | ||
| interval_list | File | ||
| scatter_count | Integer |
scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs |
|
| synonyms_file | File (Optional) | ||
| vep_cache_dir | Directory | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] | ||
| cle_vcf_filter | Boolean | ||
| tumor_sequence | https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/sequence_data.yml#sequence_data[] | tumor_sequence: MT sequencing data and readgroup information |
tumor_sequence represents the sequencing data for the MT sample as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required. |
| disclaimer_text | String (Optional) | ||
| normal_sequence | https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/sequence_data.yml#sequence_data[] | normal_sequence: WT sequencing data and readgroup information |
normal_sequence represents the sequencing data for the WT sample as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required. |
| varscan_p_value | Float (Optional) | ||
| bqsr_known_sites | File[] |
One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. |
|
| target_intervals | File | ||
| followup_sequence | https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/sequence_data.yml#sequence_data[] | ||
| summary_intervals | https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/labelled_file.yml#labelled_file[] | ||
| tumor_sample_name | String | ||
| disclaimer_version | String | ||
| normal_sample_name | String | ||
| per_base_intervals | https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/labelled_file.yml#labelled_file[] | ||
| pindel_insert_size | Integer | ||
| pindel_region_file | File | ||
| germline_tsv_prefix | String (Optional) | ||
| vep_ensembl_species | String |
ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus |
|
| vep_ensembl_version | String |
ensembl version - Must be present in the cache directory. Example: 95 |
|
| vep_to_table_fields | String[] | ||
| annotate_coding_only | Boolean (Optional) | ||
| filter_docm_variants | Boolean (Optional) |
Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls |
|
| filter_minimum_depth | Integer (Optional) | ||
| germline_coding_only | Boolean (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/labelled_file.yml#labelled_file[] | ||
| strelka_cpu_reserved | Integer (Optional) | ||
| varscan_min_coverage | Integer (Optional) | ||
| varscan_min_var_freq | Float (Optional) | ||
| vep_ensembl_assembly | String |
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
|
| varscan_strand_filter | Integer (Optional) | ||
| vep_custom_annotations | https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
| qc_minimum_base_quality | Integer (Optional) | ||
| varscan_max_normal_freq | Float (Optional) | ||
| variants_to_table_fields | String[] | ||
| emit_reference_confidence | |||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| variant_reporting_intervals | File | ||
| germline_vep_to_table_fields | String[] | ||
| picard_metric_accumulation_level | String | ||
| germline_variants_to_table_fields | String[] | ||
| variants_to_table_genotype_fields | String[] | ||
| germline_variants_to_table_genotype_fields | String[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| concordance |
../tools/concordance.cwl
(CommandLineTool)
|
Concordance checking between Tumor and Normal BAM | |
| full_report |
../tools/cle_aml_trio_report_full_variants.cwl
(CommandLineTool)
|
cle aml_trio full variants report | |
| pindel_region |
../subworkflows/pindel_region.cwl
(Workflow)
|
Run pindel on provided region | |
| coverage_report |
../tools/cle_aml_trio_report_coverage_stat.cwl
(CommandLineTool)
|
cle aml_trio hs_metrics coverage_stat report | |
| extract_freemix |
aml_trio_cle.cwl#extract_freemix/3c280c7e-2f91-44a9-b103-4990c742bfad
(ExpressionTool)
|
||
| alignment_report |
../tools/cle_aml_trio_report_alignment_stat.cwl
(CommandLineTool)
|
cle aml_trio alignment_stat report | |
| tumor_index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| normal_index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| tumor_bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| normal_bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| followup_index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| followup_bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| tumor_detect_variants |
detect_variants.cwl
(Workflow)
|
Detect Variants workflow | |
| followup_bam_readcount |
../tools/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
| tumor_alignment_and_qc |
alignment_exome.cwl
(Workflow)
|
exome alignment with qc | |
| normal_alignment_and_qc |
alignment_exome.cwl
(Workflow)
|
exome alignment with qc | |
| germline_detect_variants |
../subworkflows/germline_detect_variants.cwl
(Workflow)
|
exome alignment and germline variant detection | |
| followup_alignment_and_qc |
alignment_exome.cwl
(Workflow)
|
exome alignment with qc | |
| annotated_filter_vcf_index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| add_disclaimer_to_tumor_final_tsv |
../tools/add_string_at_line.cwl
(CommandLineTool)
|
Insert an arbitrary string at a specific line of a file | |
| add_disclaimer_to_germline_final_tsv |
../tools/add_string_at_line.cwl
(CommandLineTool)
|
Insert an arbitrary string at a specific line of a file | |
| add_disclaimer_to_full_variant_report |
../tools/add_string_at_line.cwl
(CommandLineTool)
|
Insert an arbitrary string at a specific line of a file | |
| add_disclaimer_version_to_tumor_final_tsv |
../tools/add_string_at_line.cwl
(CommandLineTool)
|
Insert an arbitrary string at a specific line of a file | |
| add_disclaimer_to_tumor_final_filtered_vcf |
../tools/add_string_at_line_bgzipped.cwl
(CommandLineTool)
|
Insert an arbitrary string at a specific line of a gzipped file | |
| add_disclaimer_version_to_germline_final_tsv |
../tools/add_string_at_line.cwl
(CommandLineTool)
|
Insert an arbitrary string at a specific line of a file | |
| add_disclaimer_version_to_full_variant_report |
../tools/add_string_at_line.cwl
(CommandLineTool)
|
Insert an arbitrary string at a specific line of a file | |
| add_disclaimer_version_to_tumor_final_filtered_vcf |
../tools/add_string_at_line_bgzipped.cwl
(CommandLineTool)
|
Insert an arbitrary string at a specific line of a gzipped file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| tumor_cram | File | ||
| normal_cram | File | ||
| followup_cram | File | ||
| tumor_final_tsv | File | ||
| tumor_final_vcf | File | ||
| tumor_flagstats | File | ||
| normal_flagstats | File | ||
| tumor_hs_metrics | File | ||
| docm_filtered_vcf | File | ||
| normal_hs_metrics | File | ||
| pindel_region_vcf | File | ||
| tumor_vep_summary | File | ||
| followup_flagstats | File | ||
| germline_final_tsv | File | ||
| germline_final_vcf | File | ||
| followup_hs_metrics | File | ||
| full_variant_report | File | ||
| mutect_filtered_vcf | File | ||
| pindel_filtered_vcf | File | ||
| coverage_stat_report | File | ||
| strelka_filtered_vcf | File | ||
| varscan_filtered_vcf | File | ||
| alignment_stat_report | File | ||
| germline_filtered_tsv | File | ||
| germline_filtered_vcf | File | ||
| mutect_unfiltered_vcf | File | ||
| pindel_unfiltered_vcf | File | ||
| strelka_unfiltered_vcf | File | ||
| varscan_unfiltered_vcf | File | ||
| tumor_final_filtered_vcf | File | ||
| tumor_summary_hs_metrics | File[] | ||
| normal_summary_hs_metrics | File[] | ||
| tumor_insert_size_metrics | File | ||
| tumor_verify_bam_id_depth | File | ||
| normal_insert_size_metrics | File | ||
| normal_verify_bam_id_depth | File | ||
| followup_summary_hs_metrics | File[] | ||
| tumor_snv_bam_readcount_tsv | File | ||
| tumor_verify_bam_id_metrics | File | ||
| followup_insert_size_metrics | File | ||
| followup_verify_bam_id_depth | File | ||
| normal_snv_bam_readcount_tsv | File | ||
| normal_verify_bam_id_metrics | File | ||
| somalier_concordance_metrics | File | ||
| tumor_indel_bam_readcount_tsv | File | ||
| tumor_mark_duplicates_metrics | File | ||
| followup_snv_bam_readcount_tsv | File | ||
| followup_verify_bam_id_metrics | File | ||
| normal_indel_bam_readcount_tsv | File | ||
| normal_mark_duplicates_metrics | File | ||
| somalier_concordance_statistics | File | ||
| tumor_alignment_summary_metrics | File | ||
| followup_indel_bam_readcount_tsv | File | ||
| followup_mark_duplicates_metrics | File | ||
| normal_alignment_summary_metrics | File | ||
| followup_alignment_summary_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/pipelines/aml_trio_cle.cwl
