Explore Workflows
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Graph | Name | Retrieved From | View |
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wf_trim_and_map_se_nostats.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_nostats.cwl Branch/Commit ID: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256 |
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assm_assm_blastn_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_assm_assm_blastn_wnode.cwl Branch/Commit ID: 8fbfb03088968846bb2c0a79ac50b231b43db64f |
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Unaligned BAM to BQSR
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bam_to_bqsr.cwl Branch/Commit ID: f9600f9959acdc30259ba7e64de61104c9b01f0b |
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cnv_manta
CNV Manta calling |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/subworkflows/cnv_manta.cwl Branch/Commit ID: cebfad2f456d672052ef8c83f5ff1b4f3b4368e4 |
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extract_gencoll_ids
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https://github.com/ncbi/pgap.git
Path: task_types/tt_extract_gencoll_ids.cwl Branch/Commit ID: 94c97cfc95a5bf102a6f9206e045ea1afb768317 |
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exome alignment with qc, no bqsr, no verify_bam_id
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/alignment_exome_nonhuman.cwl Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a |
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bacterial_orthology_cond
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https://github.com/ncbi/pgap.git
Path: bacterial_orthology/wf_bacterial_orthology_conditional.cwl Branch/Commit ID: 9362082213e20315f76f6f5c235cac3aae565747 |
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CODEX analysis pipeline using Cytokit
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https://github.com/hubmapconsortium/codex-pipeline.git
Path: steps/illumination_first_stitching.cwl Branch/Commit ID: a55bd4705b4d8a22174ae3b52aad34d6f9028feb |
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samtools_sort
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/subworkflows/samtools_sort.cwl Branch/Commit ID: cebfad2f456d672052ef8c83f5ff1b4f3b4368e4 |
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final_filtering
Final filtering |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/subworkflows/final_filtering.cwl Branch/Commit ID: cebfad2f456d672052ef8c83f5ff1b4f3b4368e4 |