Explore Workflows
View already parsed workflows here or click here to add your own
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qiime2 create phylogenetic tree
Generate a tree for phylogenetic diversity analyses from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
![]() Path: packed/qiime2-step2-dada2.cwl Branch/Commit ID: qiime2-workflow Packed ID: qiime2-05-phylogeny.cwl |
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5S-from-tablehits.cwl
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![]() Path: tools/5S-from-tablehits.cwl Branch/Commit ID: master |
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qiime2 rarefaction visualization
Alpha rarefaction plotting from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
![]() Path: packed/qiime2-step3-alpha-analysis.cwl Branch/Commit ID: qiime2-workflow-paired Packed ID: qiime2-07-alpha-rarefaction.cwl |
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workflow.cwl
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![]() Path: flow_copy2apollo-dev/workflow.cwl Branch/Commit ID: dev |
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metrics.cwl
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![]() Path: workflows/mirnaseq/metrics.cwl Branch/Commit ID: master |
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kfdrc_alignment_wf.cwl
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![]() Path: workflows/kfdrc_alignment_wf.cwl Branch/Commit ID: dev |
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TransDecoder 2 step workflow, running TransDecoder.LongOrfs (step 1) followed by TransDecoder.Predict (step2)
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![]() Path: workflows/TransDecoder-v5-wf-2steps.cwl Branch/Commit ID: fix_sbg_namespace |
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LSU-from-tablehits.cwl
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![]() Path: tools/LSU-from-tablehits.cwl Branch/Commit ID: master |
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Find reads with predicted coding sequences above 60 AA in length
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![]() Path: workflows/orf_prediction.cwl Branch/Commit ID: c1f8b22 |
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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 |