Explore Workflows

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

Graph Name Retrieved From View
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: master
workflow graph scatter-workflow.cwl

https://github.com/BiodataAnalysisGroup/intro-to-cwl-docker.git

Path: _includes/cwl/scatter-workflow.cwl

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

https://github.com/fgomez02/analysis-workflows.git

Path: definitions/subworkflows/cnvkit_single_sample.cwl

Branch/Commit ID: No_filters_detect_variants
workflow graph 05-quantification.cwl

ATAC-seq - Quantification

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/05-quantification.cwl

Branch/Commit ID: master
workflow graph qc_workflow.cwl

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/QC/qc_workflow.cwl

Branch/Commit ID: 0.0.33_dmp
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 workflow.cwl

https://github.com/Andreja28/cloud-workflows.git

Path: cwl/console-CAD/workflow.cwl

Branch/Commit ID: master
workflow graph canine_manta_module.cwl

https://github.com/d3b-center/canine-dev.git

Path: subworkflows/canine_manta_module.cwl

Branch/Commit ID: master
workflow graph oxog_sub_wf.cwl

This is a subworkflow - this is not meant to be run as a stand-alone workflow!

https://github.com/ICGC-TCGA-PanCancer/pcawg-oxog-filter.git

Path: oxog_sub_wf.cwl

Branch/Commit ID: develop
workflow graph scatter-valuefrom-wf4.cwl#main

https://github.com/common-workflow-language/common-workflow-language.git

Path: v1.0/v1.0/scatter-valuefrom-wf4.cwl

Branch/Commit ID: master

Packed ID: main