Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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tt_blastn_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_blastn_wnode.cwl Branch/Commit ID: bb2f26dfe630179737ec2ff08a8614f1f47abcaf |
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protein similarities
run diamond on mutlple DBs and merge-sort results |
https://github.com/MG-RAST/pipeline.git
Path: CWL/Workflows/protein-diamond.workflow.cwl Branch/Commit ID: 9909eaf02b93bf3c5b20d9dd18a3ec076bc7a934 |
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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: b465f0da2806ddb6df481409541d13288ccb40ec |
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downsample unaligned BAM and align
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/downsampled_alignment.cwl Branch/Commit ID: 9e5f228bc1a3d0dfe950b5d41d7e4319e834a6d4 |
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kfdrc_process_bam.cwl
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https://github.com/kids-first/kf-alignment-workflow.git
Path: subworkflows/kfdrc_process_bam.cwl Branch/Commit ID: 09c05e788df9cd77cead39892fd02140faa765a8 |
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align_sort_sa
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https://github.com/ncbi/pgap.git
Path: task_types/tt_align_sort_sa.cwl Branch/Commit ID: b12ec8c8e832151033b9e6c0a76a3c3df18d45da |
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Merge, annotate, and generate a TSV for SVs
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/merge_svs.cwl Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c |
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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: 2f0db4b3c515f91c5cfda19c78cf90d339390986 |
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varscan somatic workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/varscan.cwl Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c |
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joint genotyping for trios or small cohorts
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/joint_genotype.cwl Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c |
