Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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gcaccess_from_list
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https://github.com/ncbi/pgap.git
Path: task_types/tt_gcaccess_from_list.cwl Branch/Commit ID: d39017c63dd8e088f1ad3809d709529df602e05f |
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wf_trim_and_map_se.cwl
This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment |
https://github.com/YeoLab/eclip.git
Path: cwl/wf_trim_and_map_se.cwl Branch/Commit ID: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256 |
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gcaccess_from_list
|
https://github.com/ncbi/pgap.git
Path: task_types/tt_gcaccess_from_list.cwl Branch/Commit ID: 609aead9804a8f31fa9b3dbc7e52105aec487f31 |
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tmb.cwl
Workflow for calculating TMB tumor mutational burden on a single sample |
https://github.com/mskcc/pluto-cwl.git
Path: cwl/tmb.cwl Branch/Commit ID: d8a8af9fdb69c0a4003680c1d3b96f35d5e48f0e |
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genomics-workspace-genome.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_genomicsWorkspace/genomics-workspace-genome.cwl Branch/Commit ID: 89cff9f0d36a23bf57b3f4bdbd3ed57e3347c945 |
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workflow.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_md5checksums/workflow.cwl Branch/Commit ID: c6077d2756e628f469b446e1584ac8a86582d729 |
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WGS QC workflow nonhuman
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/qc_wgs_nonhuman.cwl Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022 |
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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: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620 |
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wf_clipseqcore_pe_1barcode.cwl
Workflow for handling reads containing one barcode. Returns the bam file containing read2 only. Notes: runs the following steps: - demultiplex - trimfirst_file2string - trimagain_file2string - b1_trim_and_map - view_r2 - index_r2_bam - make_bigwigs |
https://github.com/YeoLab/eclip.git
Path: cwl/wf_clipseqcore_pe_1barcode.cwl Branch/Commit ID: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256 |
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tmb.cwl
Workflow for calculating TMB tumor mutational burden on a single sample |
https://github.com/mskcc/pluto-cwl.git
Path: cwl/tmb.cwl Branch/Commit ID: 7eb2b0a4d37018142233d770595ac2e00376dab4 |