Explore Workflows

View already parsed workflows here or click here to add your own

Graph	Name	Retrieved From	View
	Non-Coding Bacterial Genes	https://github.com/ncbi/pgap.git Path: bacterial_noncoding/wf_bacterial_noncoding.cwl Branch/Commit ID: 5cc4af517f82f4cda3023644d61abd85cbc1fc18
	Apply filters to VCF file	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/filter_vcf_mouse.cwl Branch/Commit ID: 6b365b79675b2aabfb8d5829bb8df0a6e986b037
	qiime2 rarefaction visualization Alpha rarefaction plotting from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/	https://github.com/duke-gcb/bespin-cwl.git Path: packed/qiime2-step3-alpha-analysis.cwl Branch/Commit ID: e2dc95d4f12210359360d814382e7201d836dfcf Packed ID: qiime2-07-alpha-rarefaction.cwl
	assm_assm_blastn_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_assm_assm_blastn_wnode.cwl Branch/Commit ID: 92118627c800e4addb7e29b9dabcca073a5bae71
	FASTQ to BQSR	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/fastq_to_bqsr.cwl Branch/Commit ID: 869b331cfeb9dbd5907498e3eccdebc7c28283e5
	readgroup_fastq_pe.cwl	https://github.com/nci-gdc/gdc-dnaseq-cwl.git Path: workflows/bamfastq_align/readgroup_fastq_pe.cwl Branch/Commit ID: 0495e3095182b2e1b4d6274833b3d2ce30347a4e
	revsort.cwl Reverse the lines in a document, then sort those lines.	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/revsort.cwl Branch/Commit ID: 1eb6bfe3c77aebaf69453a669d21ae7a5a78056f
	exome alignment and somatic variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_exome_nonhuman.cwl Branch/Commit ID: 174f3b239018328cec1d821947438b457552724c
	bam-bedgraph-bigwig.cwl Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.	https://github.com/datirium/workflows.git Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5
	align_merge_sas	https://github.com/ncbi/pgap.git Path: task_types/tt_align_merge_sas.cwl Branch/Commit ID: 369afa7090a7480e6a0b144eff967a4a52b6fde2