- 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 |
|
chromosome | String |
chromosome for targeted sequencing for CODEX |
|
read_group | String (Optional) |
FASTA read group (used to fix BAM files) |
|
manta_exome | Boolean |
provide appropriate settings for WES |
|
manta_min_q | String |
minimum CNV quality for MANTA |
|
enable_codex | Boolean |
execute CODEX predictions |
|
enable_manta | Boolean |
execute MANTA predictions |
|
gridss_min_q | String |
minimum CNV quality for GRIDSS |
|
bwt_algorithm | String (Optional) |
BWT construction algorithm: bwtsw or is (Default: auto) |
|
codex_max_len | String |
maximum CNV lenght for CODEX |
|
codex_min_len | String |
minimum CNV lenght for CODEX |
|
enable_gridss | Boolean |
execute GRIDSS predictions |
|
manta_max_len | String |
maximum CNV lenght for MANTA |
|
manta_min_len | String |
minimum CNV lenght for MANTA |
|
threads_fastp | Integer (Optional) |
number of threads for fastp |
|
gridss_max_len | String |
maximum CNV lenght for GRIDSS |
|
gridss_min_len | String |
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 |
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 |
minimum CNV Bayes factor for EXOME_DEPTH |
|
exomeDepth_max_len | String |
maximum CNV lenght for EXOME_DEPTH |
|
exomeDepth_min_len | String |
minimum CNV lenght for EXOME_DEPTH |
|
min_mapping_quality | Integer |
skip alignments with MAPQ smaller than this minimum |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
bwa_mem | bwa_mem | ||
bwa_index | bwa_index | ||
cnv_codex | cnv_codex |
CNV CODEX calling |
|
cnv_manta | cnv_manta |
CNV Manta calling |
|
cnv_gridss | cnv_gridss |
CNV GRIDSS calling |
|
bam_filtering | bam_filtering |
BAM filtering |
|
samtools_sort | samtools_sort | ||
trimmed_fastq | trimmed_fastq |
Quality Control (raw data), Raw Data trimming and Quality Control (pre-processed) |
|
cnv_exomedepth | cnv_exomedepth |
CNV ExomeDepth calling |
|
final_filtering | final_filtering |
Final filtering |
|
picard_markduplicates | picard_markduplicates |
Mark duplicates |
|
samtools_view_sam2bam | 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/26ae4914651d5b3e188028d1e9d88a391b3f6730/structuralvariants/cwl/abstract_workflow/abstract_workflow.cwl