Explore Workflows
View already parsed workflows here or click here to add your own
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wf_trim_partial_and_map_se.cwl
This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment |
https://github.com/yeolab/eclip.git
Path: cwl/wf_trim_partial_and_map_se.cwl Branch/Commit ID: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256 |
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cluster_blastp_wnode and gpx_qdump combined
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https://github.com/ncbi/pgap.git
Path: task_types/tt_cluster_and_qdump.cwl Branch/Commit ID: cd97086739ae5988bab09b05e9259675c4b6bce6 |
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Hello World
Outputs a message using echo |
https://github.com/common-workflow-library/legacy.git
Path: workflows/hello/hello-param.cwl Branch/Commit ID: 767d700e602805112a4c953d166e570cddfa2605 |
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steps.cwl
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https://github.com/dimitrapanou/scrnaseq-cwl.git
Path: steps.cwl Branch/Commit ID: b8e641c2cb33197bdbdc04c9fb9cfbd818af1d94 |
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lobSTR-workflow.cwl
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https://github.com/common-workflow-library/legacy.git
Path: workflows/lobSTR/lobSTR-workflow.cwl Branch/Commit ID: 17b65ea19d81527090fded62ffa0e1ba3b25d561 |
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rRNA_selection.cwl
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https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git
Path: tools/rRNA_selection.cwl Branch/Commit ID: 43d2fb8a5430dc56b55e84e3986d0079cad8d185 |
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assm_assm_blastn_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_assm_assm_blastn_wnode.cwl Branch/Commit ID: 4b73bfeb967ee9f57a0410276f7c39e784f0846f |
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Running cellranger count and lineage inference
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/single_cell_rnaseq.cwl Branch/Commit ID: 735be84cdea041fcc8bd8cbe5728b29ca3586a21 |
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EMG pipeline v3.0 (single end version)
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https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git
Path: workflows/emg-pipeline-v3.cwl Branch/Commit ID: 886df9de6713e06228d2560c40f451155a196383 |
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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: 581156366f91861bd4dbb5bcb59f67d468b32af3 |
