Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph scatter-valuefrom-wf5.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/scatter-valuefrom-wf5.cwl

Branch/Commit ID: e62f99dd79d6cb9c157cceb458f74200da84f6e9
workflow graph kfdrc_bwamem_subwf.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/dev/ultra-opt/workflows/kfdrc_bwamem_subwf.cwl

Branch/Commit ID: 9fc3770230e1bd8495f5e6a18665bd21e7c6fafd
workflow graph main-wes_chr21_test.cwl

https://github.com/bcbio/bcbio_validation_workflows.git

Path: wes-agha-test/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl

Branch/Commit ID: master
workflow graph Per-chromosome pindel

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 51724b44c96e5fd849ae55b752865b80bc47d66c
workflow graph hi-c-processing-bam.cwl

https://github.com/4dn-dcic/pipelines-cwl.git

Path: cwl_awsem_v1/hi-c-processing-bam.cwl

Branch/Commit ID: dev2
workflow graph EMG pipeline's QIIME workflow

Step 1: Set environment PYTHONPATH, QIIME_ROOT, PATH Step 2: Run QIIME script pick_closed_reference_otus.py ${python} ${qiimeDir}/bin/pick_closed_reference_otus.py -i $1 -o $2 -r ${qiimeDir}/gg_13_8_otus/rep_set/97_otus.fasta -t ${qiimeDir}/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt -p ${qiimeDir}/cr_otus_parameters.txt Step 3: Convert new biom format to old biom format (json) ${qiimeDir}/bin/biom convert -i ${resultDir}/cr_otus/otu_table.biom -o ${resultDir}/cr_otus/${infileBase}_otu_table_json.biom --table-type=\"OTU table\" --to-json Step 4: Convert new biom format to a classic OTU table. ${qiimeDir}/bin/biom convert -i ${resultDir}/cr_otus/otu_table.biom -o ${resultDir}/cr_otus/${infileBase}_otu_table.txt --to-tsv --header-key taxonomy --table-type \"OTU table\" Step 5: Create otu summary ${qiimeDir}/bin/biom summarize-table -i ${resultDir}/cr_otus/otu_table.biom -o ${resultDir}/cr_otus/${infileBase}_otu_table_summary.txt Step 6: Move one of the result files mv ${resultDir}/cr_otus/otu_table.biom ${resultDir}/cr_otus/${infileBase}_otu_table_hdf5.biom Step 7: Create a list of observations awk '{print $1}' ${resultDir}/cr_otus/${infileBase}_otu_table.txt | sed '/#/d' > ${resultDir}/cr_otus/${infileBase}_otu_observations.txt Step 8: Create a phylogenetic tree by pruning GreenGenes and keeping observed otus ${python} ${qiimeDir}/bin/filter_tree.py -i ${qiimeDir}/gg_13_8_otus/trees/97_otus.tree -t ${resultDir}/cr_otus/${infileBase}_otu_observations.txt -o ${resultDir}/cr_otus/${infileBase}_pruned.tree

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/qiime-workflow.cwl

Branch/Commit ID: 0fed1c9
workflow graph cond-wf-003.1_nojs.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/conditionals/cond-wf-003.1_nojs.cwl

Branch/Commit ID: e62f99dd79d6cb9c157cceb458f74200da84f6e9
workflow graph rnaseq-header.cwl

https://github.com/datirium/workflows.git

Path: metadata/rnaseq-header.cwl

Branch/Commit ID: d7e214cefcfdabbe6b99d6d3d221998e0dc40e26
workflow graph Subworkflow that runs cnvkit in single sample mode and returns a vcf file

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/cnvkit_single_sample.cwl

Branch/Commit ID: 24e5290aec441665c6976ee3ee8ae3574c49c6b5
workflow graph Super-enhancer post ChIP-Seq analysis

Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)

https://github.com/datirium/workflows.git

Path: workflows/super-enhancer.cwl

Branch/Commit ID: 3fc68366adb179927af5528c27b153abaf94494d