Explore Workflows
View already parsed workflows here or click here to add your own
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trick_revsort.cwl
Reverse the lines in a document, then sort those lines. |
https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/trick_revsort.cwl Branch/Commit ID: 83038feb2a6fc3bab952e1ecc2a11bfbc8c557b4 |
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Build Bismark indices
Copy fasta_file file to the folder and run 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 input. |
https://github.com/datirium/workflows.git
Path: workflows/bismark-index.cwl Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f |
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kmer_build_tree
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_build_tree.cwl Branch/Commit ID: be9d12a3f8e1924183a1dc6a0bda6ada4195ca71 |
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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: subworkflows/allele-vcf-alignreads-se-pe.cwl Branch/Commit ID: 3b2e0de49d9ee6fd9a8c9580b6a02d0f7e4c8f7c |
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tt_kmer_top_n.cwl
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_top_n.cwl Branch/Commit ID: 3e7a3c1cc1ed5164ae0a51a96f20d7c480d1d70b |
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bam to trimmed fastqs
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315 |
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fastq2fasta.cwl
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https://github.com/arvados/bh20-seq-resource.git
Path: workflows/fastq2fasta/fastq2fasta.cwl Branch/Commit ID: 556263eae40c2371f85b482494472e165ae4d1d5 |
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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: be9d12a3f8e1924183a1dc6a0bda6ada4195ca71 |
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Seurat Cluster
Seurat Cluster ============== Runs filtering, integration, and clustering analyses for Cell Ranger Count Gene Expression or Cell Ranger Aggregate experiments. |
https://github.com/datirium/workflows.git
Path: workflows/seurat-cluster.cwl Branch/Commit ID: f3e44d3b0f198cf5245c49011124dc3b6c2b06fd |
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sequence (bam or fastqs) to trimmed fastqs
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/sequence_to_trimmed_fastq.cwl Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0 |
