Explore Workflows

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

Graph	Name	Retrieved From	View
	env-wf3.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/env-wf3.cwl Branch/Commit ID: 26870e38cec81af880cd3e4789ae6cee8fc27020
	step-valuefrom3-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl Branch/Commit ID: 09323506da219ba3ddb5313bd83022b52cac9adc
	Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)	https://github.com/ncbi/pgap.git Path: bacterial_annot/wf_bacterial_annot_pass4.cwl Branch/Commit ID: 343cb00abda2bc06daf9a32e1386c835f324ae6e
	Unaligned to aligned BAM	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/align.cwl Branch/Commit ID: 93656ed6582073e434eab168c610625a835dce37
	rna_prediction-sub-wf.cwl	https://github.com/EBI-Metagenomics/pipeline-v5.git Path: workflows/subworkflows/rna_prediction-sub-wf.cwl Branch/Commit ID: 6ec8d032feb120eb0eebf9a0c01d48deabf42eea
	bam_readcount workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bam_readcount.cwl Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0
	Feature expression merge - combines feature expression from several experiments Feature expression merge - combines feature expression from several experiments ========================================================================= Workflows merges RPKM (by default) gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns (by default). Reported unique columns are renamed based on the experiments names.	https://github.com/datirium/workflows.git Path: workflows/feature-merge.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
	allele-vcf-alignreads-se-pe.cwl Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.	https://github.com/datirium/workflows.git Path: subworkflows/allele-vcf-alignreads-se-pe.cwl Branch/Commit ID: 69623308d3b5577a4672b1d5aaf104ad1a259b20
	tt_fscr_calls_pass1	https://github.com/ncbi/pgap.git Path: task_types/tt_fscr_calls_pass1.cwl Branch/Commit ID: 807fe40bca1fbd18ede6250851b9f71de98da69b
	exome alignment and germline variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/germline_exome.cwl Branch/Commit ID: 1585504ccffafac53b1594349ed934f45206ee2b