Explore Workflows
View already parsed workflows here or click here to add your own
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main-prealign.cwl
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Path: prealign/prealign-workflow/main-prealign.cwl Branch/Commit ID: master |
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Chunked version of phmmer-v3.2.cwl
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Path: workflows/phmmer-v3.2-chunked-wf.cwl Branch/Commit ID: avoid-spaces |
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fillout_post_processing.cwl
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Path: cwl/fillout_post_processing.cwl Branch/Commit ID: master |
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functional analysis prediction with InterProScan
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Path: workflows/functional_analysis.cwl Branch/Commit ID: f993cad |
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bqsr-flow-distr.cwl
Run BQSR pre+post+plot flow with distribution |
Path: stage/bqsr-flow-distr.cwl Branch/Commit ID: master |
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genomel_cohort_gatk4.cwl
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Path: genomel/genomel_cohort_gatk4.cwl Branch/Commit ID: master |
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checker-workflow-wrapping-tool.cwl
This demonstrates how to wrap a \"real\" tool with a checker workflow that runs both the tool and a tool that performs verification of results |
Path: checker-workflow-wrapping-tool.cwl Branch/Commit ID: develop |
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pipeline.cwl
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Path: pipeline.cwl Branch/Commit ID: main |
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workflow_data.cwl
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Path: cwl/workflow_data.cwl Branch/Commit ID: pack_test |
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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 |
Path: workflows/qiime-workflow.cwl Branch/Commit ID: 708fd97 |
