Explore Workflows

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

Graph	Name	Retrieved From	View
	adapter for sequence_align_and_tag Some workflow engines won't stage files in our nested structure, so parse it out here	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/sequence_align_and_tag_adapter.cwl Branch/Commit ID: 295e7b7f51727c0f2d6cc86ce817449b2e8dba3c
	RNASelector as a CWL workflow https://doi.org/10.1007/s12275-011-1213-z	https://github.com/proteinswebteam/ebi-metagenomics-cwl.git Path: workflows/rna-selector.cwl Branch/Commit ID: caea457b17388fdc5cb088364c194504ae736bdd
	Functional analyis of sequences that match the 16S SSU	https://github.com/proteinswebteam/ebi-metagenomics-cwl.git Path: workflows/16S_functional_analysis.cwl Branch/Commit ID: caea457b17388fdc5cb088364c194504ae736bdd
	bact_get_kmer_reference	https://github.com/ncbi/pgap.git Path: task_types/tt_bact_get_kmer_reference.cwl Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb
	downsample unaligned BAM and align	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/downsampled_alignment.cwl Branch/Commit ID: e649fcb1092905c539be026a3f23c82d5b0871d2
	mpi_simple_wf.cwl Simple 2 step workflow to check that workflow steps are independently picking up on the number of processes. First run the parallel get PIDs step (on the input num procs) then run (on a single proc) the line count. This should equal the input.	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/mpi_simple_wf.cwl Branch/Commit ID: 1441c285e8a5afe399f5d52ca9059cb8bb513edb
	Tumor-Only Detect Variants workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/tumor_only_detect_variants.cwl Branch/Commit ID: e649fcb1092905c539be026a3f23c82d5b0871d2
	allele-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-alignreads-se-pe.cwl Branch/Commit ID: 94471ee6c01b7bc17102e45e56e7366c2a52acdf
	conpair-master	https://github.com/mskcc/roslin-variant.git Path: setup/cwl/conpair/0.2/conpair-master.cwl Branch/Commit ID: 7a2864f5af7723657406e4f3e94f92db09ec90fc
	waltz-workflow.cwl	https://github.com/mskcc/ACCESS-Pipeline.git Path: workflows/waltz/waltz-workflow.cwl Branch/Commit ID: 9e6eae9eb8448e68d509397a46303551a93a164d