Explore Workflows
View already parsed workflows here or click here to add your own
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mut3.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/mut3.cwl Branch/Commit ID: 8d8512061f2367c90aac67bcbf92af1061b4af59 |
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allele-alignreads-se-pe.cwl
Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted. |
https://github.com/datirium/workflows.git
Path: subworkflows/allele-alignreads-se-pe.cwl Branch/Commit ID: 6e09b4bf1ff0eb3dd1294f5578624c5a2a2b0b37 |
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EMG assembly for paired end Illumina
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: workflows/emg-pipeline-v4-assembly-metaSPAdes.cwl Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f |
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count-lines14-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.1.git
Path: tests/count-lines14-wf.cwl Branch/Commit ID: 368b562a1449e8cd39ae8b7f05926b2bfb9b22df |
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preprocess-ont.cwl
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https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2.git
Path: PreProcessing/preprocess-ont.cwl Branch/Commit ID: 3114ddd28bbee5505a9819b1a84f4896fd0b0992 |
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dna.cwl#main
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https://bitbucket.org/markrobinson96/workflows.git
Path: workflows/make-to-cwl/dna.cwl Branch/Commit ID: master Packed ID: main |
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trim-rnaseq-pe-dutp.cwl
Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file. |
https://github.com/datirium/workflows.git
Path: workflows/trim-rnaseq-pe-dutp.cwl Branch/Commit ID: cf107bc24a37883ef01b959fd89c19456aaecc02 |
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qc_workflow.cwl
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https://github.com/mskcc/ACCESS-Pipeline.git
Path: workflows/QC/qc_workflow.cwl Branch/Commit ID: bccb338be356db83ad178be2aa9634ae86cb5211 |
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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/Barski-lab/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: 5c0d21fe4f180730d4f6dd301e785bd6b00d5907 |
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compile1.cwl#main
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https://github.com/common-workflow-language/workflows.git
Path: workflows//compile/compile1.cwl Branch/Commit ID: master Packed ID: main |
