Workflow: CNV_pipeline
Fetched 2024-11-26 05:10:31 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bed | File |
capture kit |
|
| fastq1 | File[] |
FASTQ 1 list of files |
|
| fastq2 | File[] |
FASTQ 2 list of files |
|
| samples | File |
TXT file mapping cases ID, samples ID and batch |
|
| bits_set | Integer |
skip output alignments with this bits set |
|
| blacklist | File (Optional) |
BED file containing regions to ignore |
|
| read_group | String (Optional) |
FASTA read group (used to fix BAM files) |
|
| manta_exome | Boolean (Optional) |
provide appropriate settings for WES |
|
| manta_min_q | String (Optional) |
minimum CNV quality for MANTA |
|
| enable_codex | Boolean |
execute CODEX predictions |
|
| enable_manta | Boolean |
execute MANTA predictions |
|
| gridss_min_q | String (Optional) |
minimum CNV quality for GRIDSS |
|
| reference_sa | File (Optional) |
sa index reference genome |
|
| bwt_algorithm | String (Optional) |
BWT construction algorithm: bwtsw or is (Default: auto) |
|
| codex_max_len | String (Optional) |
maximum CNV lenght for CODEX |
|
| codex_min_len | String (Optional) |
minimum CNV lenght for CODEX |
|
| enable_gridss | Boolean |
execute GRIDSS predictions |
|
| manta_max_len | String (Optional) |
maximum CNV lenght for MANTA |
|
| manta_min_len | String (Optional) |
minimum CNV lenght for MANTA |
|
| reference_amb | File (Optional) |
amb index for reference genome |
|
| reference_ann | File (Optional) |
ann index for reference genome |
|
| reference_bwt | File (Optional) |
bwt index for reference genome |
|
| reference_fai | File (Optional) |
fai index for reference genome |
|
| reference_pac | File (Optional) |
pac index reference genome |
|
| threads_fastp | Integer (Optional) |
number of threads for fastp |
|
| gridss_max_len | String (Optional) |
maximum CNV lenght for GRIDSS |
|
| gridss_min_len | String (Optional) |
minimum CNV lenght for GRIDSS |
|
| threads_fastqc | Integer (Optional) |
number of threads for fastqc |
|
| threads_gridss | Integer (Optional) |
number of threads for GRIDSS |
|
| reference_fasta | File |
reference genome |
|
| threads_bwa_mem | Integer (Optional) |
number of threads for bwa-mem |
|
| codex_min_lratio | String (Optional) |
minimum CNV lratio for CODEX |
|
| threads_samtools | Integer (Optional) |
number of threads for samtools |
|
| enable_exomeDepth | Boolean |
execute EXOME_DEPTH predictions |
|
| exomeDepth_min_bf | String (Optional) |
minimum CNV Bayes factor for EXOME_DEPTH |
|
| exomeDepth_max_len | String (Optional) |
maximum CNV lenght for EXOME_DEPTH |
|
| exomeDepth_min_len | String (Optional) |
minimum CNV lenght for EXOME_DEPTH |
|
| min_mapping_quality | Integer |
skip alignments with MAPQ smaller than this minimum |
|
| generate_bwa_indexes | Boolean (Optional) |
enable generation of reference genome indexes |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bwa_mem |
subworkflows/bwa_mem.cwl
(Workflow)
|
bwa_mem | |
| bwa_index |
subworkflows/bwa_index.cwl
(Workflow)
|
bwa_index |
Modified from https://github.com/kids-first/kf-somatic-workflow/blob/master/sub_workflows/prepare_reference.cwl |
| cnv_codex |
subworkflows/cnv_codex.cwl
(Workflow)
|
cnv_codex |
CNV CODEX calling |
| cnv_manta |
subworkflows/cnv_manta.cwl
(Workflow)
|
cnv_manta |
CNV Manta calling |
| cnv_gridss |
subworkflows/cnv_gridss.cwl
(Workflow)
|
cnv_gridss |
CNV GRIDSS calling |
| bam_filtering |
subworkflows/bam_filtering.cwl
(Workflow)
|
bam_filtering |
BAM filtering |
| samtools_sort |
subworkflows/samtools_sort.cwl
(Workflow)
|
samtools_sort | |
| trimmed_fastq |
subworkflows/trimmed_fastq.cwl
(Workflow)
|
trimmed_fastq |
Quality Control (raw data), Raw Data trimming and Quality Control (pre-processed) |
| cnv_exomedepth |
subworkflows/cnv_exome_depth.cwl
(Workflow)
|
cnv_exomedepth |
CNV ExomeDepth calling |
| final_filtering |
subworkflows/final_filtering.cwl
(Workflow)
|
final_filtering |
Final filtering |
| picard_markduplicates |
subworkflows/picard_markduplicates.cwl
(Workflow)
|
picard_markduplicates |
Mark duplicates |
| samtools_view_sam2bam |
subworkflows/samtools_view_sam2bam.cwl
(Workflow)
|
samtools_view_sam2bam |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_all | File | ||
| html_report | File[] | ||
| json_report | File[] | ||
| output_codex | File (Optional) | ||
| output_manta | File (Optional) | ||
| output_gridss | File (Optional) | ||
| fastqc_raw_zip | File[] | ||
| fastqc_raw_html | File[] | ||
| fastqc_paired_zip | File[] | ||
| output_exomedepth | File (Optional) | ||
| fastqc_paired_html | File[] | ||
| output_bam_filtering | File[] |
https://w3id.org/cwl/view/git/93fbc4e51770d953fc44104a7b09436f75719470/structuralvariants/cwl/workflow.cwl
