Workflow: gatk-4.0.0.0-joint-calling.cwl
Fetched 2024-05-02 23:13:10 GMT
Verified with cwltool version 3.1.20221201130942
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- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| intervals | File[] |
List of intervals_list files |
|
| reference | File |
The reference file for all the samples |
|
| gvcf_files | c52f3d8bf90fee3856d1d0c55e23661e[] |
Array of array of GVCF files. Each inner array contains vcfs called for the corresponding interval\ in the interval input. The outer array represents each sample. |
|
| output_filename | String |
The name of the output VCF to produce |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| concat_multisample_gvcfs |
../tools/bcftools/bcftools-concat.cwl
(CommandLineTool)
|
About: Concatenate or combine VCF/BCF files. All source files must have the same sample
columns appearing in the same order. The program can be used, for example, to
concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel
VCF into one. The input files must be sorted by chr and position. The files
must be given in the correct order to produce sorted VCF on output unless
the -a, --allow-overlaps option is specified. |
|
| transpose_gvcf_files_list |
../expression-tools/matrix_transpose.cwl
(CommandLineTool)
|
Transpose a given matrix |
|
| index_multisample_gvcfs_csi |
../tools/bcftools/bcftools-index.cwl
(CommandLineTool)
|
About: Creates index for bgzip compressed VCF/BCF files for random access. CSI (coordinate-sorted index) is created by default. The CSI format supports indexing of chromosomes up to length 2^31. TBI (tabix index) index files, which support chromosome lengths up to 2^29, can be created by using the -t/--tbi option or using the tabix program packaged with htslib. When loading an index file, bcftools will try the CSI first and then the TBI. |
|
| index_multisample_gvcfs_tbi |
../tools/bcftools/bcftools-index-tbi.cwl
(CommandLineTool)
|
About: Creates index for bgzip compressed VCF/BCF files for random access using TBI (tabix index) index files, which support chromosome lengths up to 2^29. |
|
| combine_multisample_gvcf_indices |
../expression-tools/combine_files.cwl
(ExpressionTool)
|
Step to put secondary input files in the same folder as a main file |
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| flatten-multisample-gvcf-outputs |
../expression-tools/flatten-array-file.cwl
(ExpressionTool)
|
Transpose a given array |
|
| genomicsdbimport-and-genotype-gvcfs-per-interval-list |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| out | File |
https://w3id.org/cwl/view/git/c822e40575ecd7fc65626a73363f3bbc193b9a74/cwl/workflows/gatk-4.0.0.0-joint-calling.cwl
