Explore Workflows
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Cellranger aggr - aggregates data from multiple Cellranger runs
Devel version of Single-Cell Cell Ranger Aggregate ================================================== Workflow calls \"cellranger aggr\" command to combine output files from \"cellranger count\" (the molecule_info.h5 file from each run) into a single feature-barcode matrix containing all the data. When combining multiple GEM wells, the barcode sequences for each channel are distinguished by a GEM well suffix appended to the barcode sequence. Each GEM well is a physically distinct set of GEM partitions, but draws barcode sequences randomly from the pool of valid barcodes, known as the barcode whitelist. To keep the barcodes unique when aggregating multiple libraries, we append a small integer identifying the GEM well to the barcode nucleotide sequence, and use that nucleotide sequence plus ID as the unique identifier in the feature-barcode matrix. For example, AGACCATTGAGACTTA-1 and AGACCATTGAGACTTA-2 are distinct cell barcodes from different GEM wells, despite having the same barcode nucleotide sequence. This number, which tells us which GEM well this barcode sequence came from, is called the GEM well suffix. The numbering of the GEM wells will reflect the order that the GEM wells were provided in the \"molecule_info_h5\" and \"gem_well_labels\" inputs. When combining data from multiple GEM wells, the \"cellranger aggr\" pipeline automatically equalizes the average read depth per cell between groups before merging. This approach avoids artifacts that may be introduced due to differences in sequencing depth. It is possible to turn off normalization or change the way normalization is done through the \"normalization_mode\" input. The \"none\" value may be appropriate if you want to maximize sensitivity and plan to deal with depth normalization in a downstream step. |
https://github.com/datirium/workflows.git
Path: workflows/cellranger-aggr.cwl Branch/Commit ID: 09267e79fd867aa68a219c69e6db7d8e2e877be2 |
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word-mapping-test-files-wf.cwl#word-mapping-wf.cwl
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https://github.com/KBNLresearch/ochre.git
Path: ochre/cwl/word-mapping-test-files-wf.cwl Branch/Commit ID: bfd504ae910fbf7a3492f53430a1c9f3c3c97470 Packed ID: word-mapping-wf.cwl |
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mutect parallel workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/mutect.cwl Branch/Commit ID: 2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71 |
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exome alignment and germline variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/germline_exome.cwl Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325 |
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Alignment without BQSR
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/sequence_to_bqsr_nonhuman.cwl Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325 |
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CLE gold vcf evaluation workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/vcf_eval_cle_gold.cwl Branch/Commit ID: 2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71 |
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group-isoforms-batch.cwl
Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored. |
https://github.com/datirium/workflows.git
Path: tools/group-isoforms-batch.cwl Branch/Commit ID: 5e7385b8cfa4ddae822fff37b6bd22eb0370b389 |
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exome alignment with qc
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/alignment_exome.cwl Branch/Commit ID: 39ac49f5d080bbb6bfa97246f46a5b621254f622 |
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bwa_pe.cwl
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https://github.com/NCI-GDC/gdc-dnaseq-cwl.git
Path: workflows/align/bwa_pe.cwl Branch/Commit ID: 27a6d99cd517538eb345e2319d0903a864ea5965 |
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Varscan Workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f |
