Explore Workflows
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| Graph | Name | Retrieved From | View |
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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: 12e5256de1b680c551c87fd5db6f3bc65428af67 |
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CNV_pipeline
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/workflow.cwl Branch/Commit ID: 93fbc4e51770d953fc44104a7b09436f75719470 |
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CNV_pipeline
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/abstract_workflow/abstract_workflow.cwl Branch/Commit ID: f4c51a054b1ec51d07d89c6a8218e610653675f3 |
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protein annotation
Proteins - predict, cluster, identify, annotate |
https://github.com/MG-RAST/pipeline.git
Path: CWL/Workflows/protein-annotation.workflow.cwl Branch/Commit ID: f5839797da8209a9d3e441023f88130219751020 |
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kmer_cache_store
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_cache_store.cwl Branch/Commit ID: 909f26beaf96c2cdfe208f87ecd1e9c3de20b81c |
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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: 7f857f7f2d7c080d27c775b67a6d6f7d94bce31f |
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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: c711498c04d6b8ddf92ddceb6219f074765f7993 |
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bam-bedgraph-bigwig.cwl
Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow. |
https://github.com/datirium/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67 |
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copy_outputs.cwl
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https://github.com/mskcc/argos-cwl.git
Path: workflows/copy_outputs.cwl Branch/Commit ID: cf4867f47da089ba545aa10432fd95d7e2d20126 |
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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: a839eb6390974089e1a558c49fc07b4c66c50767 |
