Explore Workflows

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: 708fd97

https://github.com/cancerit/workflow-seq-import.git

Path: cwls/chksum_xam_to_interleaved_fq.cwl

Branch/Commit ID: 0.4.1

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines12-wf.cwl

Branch/Commit ID: main

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines11-wf-noET.cwl

Branch/Commit ID: main

Validate the telescope simulation model as a whole.

https://github.com/gammasim/workflows.git

Path: workflows/ValidateTelescopeSimulationModel.cwl

Branch/Commit ID: main

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: workflows/cmsearch-multimodel.cwl

Branch/Commit ID: 71d9c83

https://github.com/duke-gcb/bespin-cwl.git

Path: subworkflows/exomeseq-03-organizedirectories.cwl

Branch/Commit ID: gatk4-fixes

https://github.com/common-workflow-language/common-workflow-language.git

Path: v1.0/v1.0/dynresreq-workflow-inputdefault.cwl

Branch/Commit ID: master

https://github.com/genome/cancer-genomics-workflow.git

Path: detect_variants/detect_variants.cwl

Branch/Commit ID: toil_compatibility

https://github.com/ifishlin/Benchmarking_CWL.git

Path: workflows/bwameth/bwameth_mulitlib_start_with_trimmed.cwl

Branch/Commit ID: main