Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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gcaccess_from_list
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https://github.com/ncbi/pgap.git
Path: task_types/tt_gcaccess_from_list.cwl Branch/Commit ID: 041a234a935c7af7d3db95353ef80c61c88fc010 |
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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: 708fd971bd3abe4d367e501583b964bc4c0311b9 |
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WGS QC workflow mouse
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/subworkflows/qc_wgs_mouse.cwl Branch/Commit ID: 233f026ffce240071edda526391be0c03186fce8 |
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count-lines1-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/count-lines1-wf.cwl Branch/Commit ID: 78fe9d41ee5a44f8725dfbd7028e4a5ee42949cf |
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extract_gencoll_ids
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https://github.com/ncbi/pgap.git
Path: task_types/tt_extract_gencoll_ids.cwl Branch/Commit ID: 2229f26ec424f9ebeb3db7fec3bd3f84a38c7485 |
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any-type-compat.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/any-type-compat.cwl Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7 |
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alignment for mouse with qc
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/pipelines/alignment_wgs_mouse.cwl Branch/Commit ID: 233f026ffce240071edda526391be0c03186fce8 |
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Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: 195b4ab487c939eb32a55d9f78bc1befd100caae |
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gathered exome alignment and somatic variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/somatic_exome_gathered.cwl Branch/Commit ID: 04d21c33a5f2950e86db285fa0a32a6659198d8a |
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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: 0fed1c959ab33112eae46fb02fceffa8bb26b811 |
