Explore Workflows
View already parsed workflows here or click here to add your own
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CODEX analysis pipeline using Cytokit
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Path: steps/ometiff_second_stitching.cwl Branch/Commit ID: no-gpu-for-cwl-vis-only |
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pipeline-se-blacklist-removal.cwl
ATAC-seq pipeline - reads: SE - with blacklist removal |
Path: v1.0/ATAC-seq_pipeline/pipeline-se-blacklist-removal.cwl Branch/Commit ID: master |
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create_snap_and_analyze.cwl
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Path: create_snap_and_analyze.cwl Branch/Commit ID: 44dbe38 |
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alignment_workflow.cwl
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Path: aligner/topmed-cwl/workflow/alignment_workflow.cwl Branch/Commit ID: develop |
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geogrid_workflow.cwl
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Path: workflows/geogrid_workflow.cwl Branch/Commit ID: develop |
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fusion_workflow.cwl
Fusion workflow, runs STARFusion and Arriba |
Path: fusion_workflow.cwl Branch/Commit ID: 1.0.0 |
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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: 3168316 |
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Detect Variants workflow for WGS pipeline
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Path: definitions/pipelines/detect_variants_wgs.cwl Branch/Commit ID: downsample_and_recall |
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scatter-valuefrom-wf2.cwl
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Path: tests/scatter-valuefrom-wf2.cwl Branch/Commit ID: main |
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05-quantification.cwl
ATAC-seq - Quantification |
Path: v1.0/ATAC-seq_pipeline/05-quantification.cwl Branch/Commit ID: master |
