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CWL for GDC DNASeq workflows

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# GDC DNA-Seq Alignment Workflow

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This workflow takes a set of input WGS/WXS/Targeted Sequencing FASTQ/BAM files and generates
a harmonized BAM file and an sqlite database of various metrics collected.
## License Note
This repository is licensed under Apache License Version 2.0. Exceptions are code blocks licensed under CC-BY-SA-4.0. 
The CC-BY-SA-4.0 code blocks are denoted by `/begin <AUTHOR> CC-BY-SA-4.0` to `/end <AUTHOR> CC-BY-SA-4.0`.

## Environment

### Pre-requisites

Workflow development requires the following programs installed:

- `docker`
- `just`
- `python>=3.8`
  - `cwltool==3.1.20230213100550`

These workflows are developed and tested on Ubuntu.

* Ubuntu 20.04

The CWL is developed for `cwltools` version `3.1.20230213100550`
 
https://www.commonwl.org/

## GDC Users

There are two entry points:
 - harmonization of FASTQ and BAM data: `gdc-dnaseq-aln-cwl/gdc_dnaseq.bamfastq_align.workflow.cwl`.
 - trusted pre-aligned data: `gdc-dnaseq-prealn-cwl/gdc_dnaseq.aligned_reads.workflow.cwl`.

## For external users

The repository has only been tested on GDC data and in the particular environment GDC is running in. Some of the reference data required for the workflow production are hosted in [GDC reference files](https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files "GDC reference files"). For any questions related to GDC data, please contact the GDC Help Desk at support@nci-gdc.datacommons.io.

The entrypoint CWL workflow for external users is `subworkflows/main/gdc_dnaseq_main_workflow.cwl`.

An example input yaml is available here: `example/gdc_dnaseq_main_workflow_example_input.yaml`.

### Inputs

| Name | Type | Description |
| ---- | ---- | ----------- |
| `bam_name` | `string` | basename of the final harmonized bam |
| `job_uuid` | `string` | unique identifier for the workflow run |
| `collect_wgs_metrics` | `boolean` | set to `true` to generate metrics for WGS data |
| `amplicon_kit_set_file_list` | `amplicon_kit_set_file[]` | array of objects containing the paths to the amplicon and target files (only for amplicon-based targeted/WXS sequencing) |
| `capture_kit_set_file_list` | `capture_kit_set_file[]` | array of objects containing the paths to the target and bait files (only for hybrid-selection targeted/WXS sequencing) |
| `readgroup_fastq_pe_file_list` | `readgroup_fastq_file[]` | array of objects containing the paths to paired-end fastq files and their associated readgroup metadata |
| `readgroup_fastq_se_file_list` | `readgroup_fastq_file[]` | array of objects containing the paths to single-end fastq files and their associated readgroup metadata |
| `readgroups_bam_file_list` | `readgroups_bam_file[]` | array of objects containing the paths to BAM files and their associated readgroup metadata |
| `common_biallelic_vcf` | `File` | tabix-indexed common biallelic VCF (e.g., gnomad) |
| `known_snp` | `File` | tabix-indexed dbSNP VCF |
| `run_markduplicates` | `boolean` | this should be `true` in all cases except for amplicon-based PCR sequencing libraries |
| `reference_sequence` | `File` | the reference fasta file and its associated BWA/fai/dict index files |
| `thread_count` | `long` | the number of cores to use for multi-threaded tools |

**Custom Data Types**

* `amplicon_kit_set_file` - contains amplicon sequencing kit files

| Name | Type | Description |
| ---- | ---- | ----------- |
| `amplicon_kit_amplicon_file` | `File` | amplicon baits interval file |
| `amplicon_kit_target_file` | `File` | amplicon target interval file |

* `capture_kit_set_file` - contains the hybrid-selection targeted squencing kit files

| Name | Type | Description |
| ---- | ---- | ----------- |
| `capture_kit_bait_file` | `File` | capture kit baits interval file |
| `capture_kit_target_file` | `File` | capture kit targets interval file |

* `readgroup_fastq_file` - contains readgroup level fastq files and the associated readgroup metadata

| Name | Type | Description |
| ---- | ---- | ----------- |
| `forward_fastq` | `File` | required R1 fastq file |
| `reverse_fastq` | `File?` | optional R2 fastq file (for paired-end reads) |
| `readgroup_meta` | `readgroup_meta` | object containing the readgroup metadata |

* `readgroups_bam_file` - contains a BAM file and the associated readgroup metadata

| Name | Type | Description |
| ---- | ---- | ----------- |
| `bam` | `File` | the BAM file |
| `readgroup_meta_list` | `readgroup_meta[]` | array of objects containing the readgroup metadata |

* `readgroup_meta` - contains readgroup metadata

| Name | Type | Description |
| ---- | ---- | ----------- |
| `CN` | `string?` | optional sequencing center |
| `DS` | `string?` | optional description |
| `DT` | `string?` | optional ISO8601 sequencing date |
| `FO` | `string?` | optional flow order array of nocleotide bases that corresponded to the nucleotides used for each flow of each read |
| `ID` | `string` | required read group ID |
| `KS` | `string?` | optional array of nucleotide bases that correspond to the key sequence of each read |
| `LB` | `string?` | optional library ID |
| `PI` | `string?` | optional predicted median insert size |
| `PL` | `string` | required platform |
| `PM` | `string?` | optional platform model |
| `PU` | `string?` | optional platform unit |
| `SM` | `string` | required sample ID |

### Outputs

| Name | Type | Description |
| ---- | ---- | ----------- |
| `output_bam` | `File` | harmonized and indexed BAM file |
| `sqlite` | `File` | sqlite file containing metrics data |

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