Explore Workflows
View already parsed workflows here or click here to add your own
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Gathered Downsample and HaplotypeCaller
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/gathered_downsample_and_recall.cwl Branch/Commit ID: ef7f3345b352319ec22dffba26c79df033b141f9 |
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Genelists heatmap - RNA-seq expression data visualized
# Genelists heatmap - RNA-seq expression data visualized This visualization workflow takes as input 1 or more genelists derived from the DESeq and/or diffbind workflows along with user-selected samples and visualizes RNA-Seq expression data in a single morpheus heatmap. ### __References__ - Morpheus, https://software.broadinstitute.org/morpheus |
https://github.com/datirium/workflows.git
Path: workflows/genelists-deseq-only.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895 |
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scatter-valuefrom-wf2.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf2.cwl Branch/Commit ID: 6300a49ec29be956ab451311fe9781522f461aee |
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io-int-default-tool-and-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/io-int-default-tool-and-wf.cwl Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4 |
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umi molecular alignment workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/molecular_qc.cwl Branch/Commit ID: ec5355f335852e51c6938809c16ea1d230a3f983 |
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FastQC - a quality control tool for high throughput sequence data
FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application |
https://github.com/datirium/workflows.git
Path: workflows/fastqc.cwl Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081 |
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Whole genome alignment and somatic variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/somatic_wgs.cwl Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb |
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heatmap-prepare.cwl
Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order. |
https://github.com/datirium/workflows.git
Path: tools/heatmap-prepare.cwl Branch/Commit ID: 46d3d403ddb240d5a8f4f31ab992b6d6a2686745 |
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bam to trimmed fastqs and biscuit alignments
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl Branch/Commit ID: 51724b44c96e5fd849ae55b752865b80bc47d66c |
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exome alignment and somatic variant detection for cle purpose
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/cle_somatic_exome.cwl Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f |
