Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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Generate genome indices for Bismark
Run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome folder name. |
https://github.com/datirium/workflows.git
Path: workflows/bismark-indices.cwl Branch/Commit ID: 2b8146f76595f0c4d8bf692de78b21280162b1d0 |
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allele-process-reference.cwl
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https://github.com/Barski-lab/workflows.git
Path: subworkflows/allele-process-reference.cwl Branch/Commit ID: f2aee86fecd321efc6857b124350f079238ea2ba |
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workflow_input_format_expr_v1_1.cwl
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/workflow_input_format_expr_v1_1.cwl Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507 |
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bam to trimmed fastqs and HISAT alignments
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl Branch/Commit ID: ec45fad68ca10fb64d5c58e704991b146dc31d28 |
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kmer_seq_entry_extract_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d |
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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: workflows/allele-vcf-alignreads-se-pe.cwl Branch/Commit ID: 4b8bb1a1ec39056253ca8eee976078e51f4a954e |
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Detect Variants workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/detect_variants.cwl Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f |
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FASTQ Download
FASTQ Download Assists in downloading problematic single-cell sequencing data from Sequence Read Archive (SRA) |
https://github.com/datirium/workflows.git
Path: workflows/fastq-download.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895 |
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advanced-header.cwl
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https://github.com/datirium/workflows.git
Path: metadata/advanced-header.cwl Branch/Commit ID: d7e214cefcfdabbe6b99d6d3d221998e0dc40e26 |
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Replace legacy AML Trio Assay
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/cle_aml_trio.cwl Branch/Commit ID: aba52e94b6d7470132d3c092c26d67e29d615300 |
