Explore Workflows

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/somatic_subpipeline.cwl

Branch/Commit ID: master

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: 3168316

Alpha rarefaction plotting from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

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

Path: packed/qiime2-step3-alpha-analysis.cwl

Branch/Commit ID: qiime2-workflow-paired

Packed ID: qiime2-07-alpha-rarefaction.cwl

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

Path: tools/collate_unique_SSU_headers.cwl

Branch/Commit ID: 3039744

https://github.com/YeoLab/sailor.git

Path: CWL-SINGULARITY-pipeline-building-code/cwl/rnaediting1strand.cwl

Branch/Commit ID: 6f21086

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

Path: tests/count-lines17-wf.cwl

Branch/Commit ID: main

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

Path: workflows/cmsearch-multimodel.cwl

Branch/Commit ID: master

https://github.com/hubmapconsortium/celldive-pipeline.git

Path: pipeline.cwl

Branch/Commit ID: cd2f15f

Process an input file to from DL0 to separate DL1 and DL2 outputs.

https://gitlab.cta-observatory.org/cta-computing/dpps/dpps-workflows.git

Path: datapipe/workflow_dl0_to_dl2.cwl

Branch/Commit ID: autoupdated

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

Path: tests/conditionals/cond-wf-006_nojs.cwl

Branch/Commit ID: main