Workflow: CNV_FPS
Fetched 2023-01-04 17:31:10 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 file |
|
| fastq2 | File[] |
FASTQ file |
|
| samples | File |
TXT file mapping samples per batch |
|
| bits_set | Integer |
skip output alignments with this bits set |
|
| blacklist | File (Optional) |
BED file containing regions to ignore for GRIDSS |
|
| chromosome | String |
chromosome for targeted sequencing for CODEX |
|
| read_group | String |
parse header which should correlate to FASTQ files |
|
| manta_exome | Boolean |
disable all high depth filters |
|
| manta_min_q | String |
minimum quality for MANTA's filter |
|
| gridss_min_q | String |
minimum quality for GRIDSS's filter |
|
| codex_max_len | String |
maximum lenght for CODEX's filter |
|
| codex_min_len | String |
minimum lenght for CODEX's filter |
|
| manta_max_len | String |
maximum lenght for MANTA's filter |
|
| manta_min_len | String |
minimum lenght for MANTA's filter |
|
| threads_fastp | Integer (Optional) |
number of threads for fastp |
|
| gridss_max_len | String |
maximum lenght for GRIDSS's filter |
|
| gridss_min_len | String |
minimum lenght for GRIDSS's filter |
|
| 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 |
minimum lratio for CODEX's filter |
|
| exomeDepth_min_q | String |
minimum quality for EXOME_DEPTH's filter |
|
| threads_samtools | Integer (Optional) |
number of threads for samtools |
|
| exomeDepth_max_len | String |
maximum lenght for EXOME_DEPTH's filter |
|
| exomeDepth_min_len | String |
minimum lenght for EXOME_DEPTH's filter |
|
| min_mapping_quality | Integer |
skip alignments with MAPQ smaller than this minimum |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bwa_mem |
subworkflows/bwa_mem.cwl
(Workflow)
|
bwa_mem | |
| bwa_index |
subworkflows/bwa_index.cwl
(Workflow)
|
bwa_index | |
| cnv_codex |
subworkflows/cnv_codex.cwl
(Workflow)
|
cnv_codex |
CNV CODEX2 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 and Raw Data trimming |
| cnv_exomedepth |
subworkflows/cnv_exome_depth.cwl
(Workflow)
|
cnv_exomedepth |
CNV ExomeDepth calling |
| 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 |
|---|---|---|---|
| html_report | File[] | ||
| json_report | File[] | ||
| output_codex | File[] | ||
| output_manta | File[] | ||
| output_gridss | File[] | ||
| fastqc_raw_zip | File[] | ||
| fastqc_raw_html | File[] | ||
| fastqc_paired_zip | File[] | ||
| output_exomedepth | File[] | ||
| fastqc_paired_html | File[] | ||
| output_bam_filtering | File[] |
https://w3id.org/cwl/view/git/1a8c6bc41c83476a5496bbaca5c3d870cfd8c21e/structuralvariants/workflow.cwl
