Explore Workflows

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

Graph Name Retrieved From View
workflow graph Merge, annotate, and generate a TSV for SVs

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: downsample_and_recall
workflow graph EMG assembly for paired end Illumina

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

Path: workflows/emg-assembly.cwl

Branch/Commit ID: master
workflow graph bulk-atac-seq-pipeline.cwl

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: bulk-atac-seq-pipeline.cwl

Branch/Commit ID: 102d8cb
workflow graph cond-wf-003.1.cwl

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

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

Branch/Commit ID: main
workflow graph GATK-Sub-Workflow-h3abionet-indel-no-vqsr.cwl

https://github.com/h3abionet/h3agatk.git

Path: workflows/GATK/GATK-Sub-Workflow-h3abionet-indel-no-vqsr.cwl

Branch/Commit ID: 1.0.1
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 03-map-pe.cwl

ChIP-seq 03 mapping - reads: PE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/03-map-pe.cwl

Branch/Commit ID: master
workflow graph functional analysis prediction with InterProScan

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/functional_analysis.cwl

Branch/Commit ID: 3f85843
workflow graph collapsed_fastq_to_bam.cwl

https://github.com/mskcc/Innovation-Pipeline.git

Path: workflows/marianas/collapsed_fastq_to_bam.cwl

Branch/Commit ID: master
workflow graph workflow.cwl

https://github.com/inab/Wetlab2Variations.git

Path: cwl-workflows/demonstrator/workflow.cwl

Branch/Commit ID: master