Explore Workflows
View already parsed workflows here or click here to add your own
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workflow.cwl
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Path: CWL/workflow.cwl Branch/Commit ID: master |
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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. |
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: master |
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pipeline.cwl
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Path: pipeline.cwl Branch/Commit ID: 5224e3a |
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picard_markduplicates
Mark duplicates |
Path: structuralvariants/cwl/subworkflows/picard_markduplicates.cwl Branch/Commit ID: 1.0.6 |
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workflow.cwl
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Path: flow_download/workflow.cwl Branch/Commit ID: master |
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contig construction and protein prediction
\"This workflow performs construction of metagenomic contigs and prediction protein sequences for metagenomic contigs. It executes 2 processes: contig construction and protein prediction. related CWL file: ./Tools/06_bwa_mem.cwl ./Tools/07_samtools_sort.cwl ./Tools/08_samtools_flagstat.cwl\" |
Path: Workflow/metagenomic_contig_mapping_sw.cwl Branch/Commit ID: main |
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bulk_analysis.cwl
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Path: steps/bulk_analysis.cwl Branch/Commit ID: d0e845d |
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rRNA_selection.cwl
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Path: tools/rRNA_selection.cwl Branch/Commit ID: master |
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umi duplex alignment fastq workflow
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Path: definitions/pipelines/alignment_umi_duplex.cwl Branch/Commit ID: master |
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genomel_cohort_gatk4.cwl
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Path: genomel/genomel_cohort_gatk4.cwl Branch/Commit ID: master |
