subworkflows

List of subworkflows CWLs

This list is auto-generated. Do not edit.

CWL	Description
align.cwl	Unaligned to aligned BAM
align_sort_markdup.cwl	Unaligned bam to sorted, markduped bam
bam_readcount.cwl	bam_readcount workflow
bam_to_trimmed_fastq_and_biscuit_alignments.cwl	bam to trimmed fastqs and biscuit alignments
bgzip_and_index.cwl	bgzip and index VCF
bisulfite_qc.cwl	Bisulfite QC tools
cellranger_mkfastq_and_count.cwl	running cellranger mkfastq and count
cnvkit_single_sample.cwl	Subworkflow that runs cnvkit in single sample mode and returns a vcf file
cram_to_bam_and_index.cwl	cram_to_bam workflow
cram_to_cnvkit.cwl	Subworkflow to allow calling cnvkit with cram instead of bam files
docm_cle.cwl	Detect Docm variants
docm_germline.cwl	Detect DoCM variants
duplex_alignment.cwl	umi duplex alignment workflow
filter_vcf.cwl	Apply filters to VCF file
filter_vcf_nonhuman.cwl	Apply filters to VCF file
fp_filter.cwl	fp_filter workflow
gatk_haplotypecaller_iterator.cwl	scatter GATK HaplotypeCaller over intervals
generate_fda_metrics.cwl	Calculate FDA-requested metrics on all aligned and unaligned sequence files
germline_detect_variants.cwl	exome alignment and germline variant detection
germline_filter_vcf.cwl	Apply filters to VCF file
hs_metrics.cwl	HS Metrics workflow
joint_genotype.cwl	joint genotyping for trios or small cohorts
merge_svs.cwl	Merge, annotate, and generate a TSV for SVs
molecular_alignment.cwl	umi molecular alignment workflow
molecular_qc.cwl	umi molecular alignment workflow
mutect.cwl	mutect parallel workflow
phase_vcf.cwl	phase VCF
pindel.cwl	pindel parallel workflow
pindel_cat.cwl	Per-region pindel
pindel_region.cwl	Run pindel on provided region
pvacseq.cwl	Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs
qc_exome.cwl	Exome QC workflow
qc_exome_no_verify_bam.cwl	Exome QC workflow
qc_wgs.cwl	WGS QC workflow
qc_wgs_nonhuman.cwl	WGS QC workflow nonhuman
sequence_align_and_tag_adapter.cwl	adapter for sequence_align_and_tag
sequence_to_bqsr.cwl	Raw sequence data to BQSR
sequence_to_bqsr_nonhuman.cwl	Alignment without BQSR
sequence_to_trimmed_fastq.cwl	sequence (bam or fastqs) to trimmed fastqs
sequence_to_trimmed_fastq_and_hisat_alignments.cwl	sequence (bam or fastqs) to trimmed fastqs and HISAT alignments
single_cell_rnaseq.cwl	Running cellranger count and lineage inference
single_sample_sv_callers.cwl	Subworkflow to allow calling different SV callers which require bam files as inputs
strelka_and_post_processing.cwl	strelka workflow
strelka_process_vcf.cwl	process VCF workflow
sv_depth_caller_filter.cwl	Filter single sample sv vcf from depth callers(cnvkit/cnvnator)
sv_paired_read_caller_filter.cwl	Filter single sample sv vcf from paired read callers(Manta/Smoove)
umi_alignment.cwl	umi per-lane alignment subworkflow
varscan.cwl	varscan somatic workflow
varscan_germline.cwl	Varscan Workflow
varscan_pre_and_post_processing.cwl	Varscan Workflow
vcf_eval_cle_gold.cwl	CLE gold vcf evaluation workflow
vcf_eval_concordance.cwl	Vcf concordance evaluation workflow
vcf_readcount_annotator.cwl	Add snv and indel bam-readcount files to a vcf