Explore Workflows

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

Graph Name Retrieved From View
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
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: 316831663e84623eb0e3a260af252fef441924d4
workflow graph fp_filter workflow

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph assm_assm_blastn_wnode

https://github.com/ncbi/pgap.git

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 6fad27f92dd604eca0e341178f594a560d70953b
workflow graph fp_filter workflow

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a
workflow graph exome alignment with qc

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

Path: definitions/pipelines/alignment_exome.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph strelka workflow

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

Path: definitions/subworkflows/strelka_and_post_processing.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph align_and_count_multiple_report.cwl

https://github.com/common-workflow-lab/wdl-cwl-translator.git

Path: wdl2cwl/tests/cwl_files/align_and_count_multiple_report.cwl

Branch/Commit ID: 0e2aa9ed4acb6a14ca5722e81b2eb4bfb303e153
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370