Explore Workflows

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

Path: tests/wf-loadContents4.cwl

Branch/Commit ID: main

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

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 5e82174

https://github.com/DataBiosphere/topmed-workflows.git

Path: aligner/topmed-cwl/workflow/alignment_workflow.cwl

Branch/Commit ID: develop

DNAseq pipeline from fastq to vcf

https://github.com/Sentieon/Sentieon-cwl.git

Path: pipeline/pipeline-fastq2vcf-opt.cwl

Branch/Commit ID: master

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

Path: tests/step-valuefrom2-wf.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: 0fed1c9

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/subworkflows/snps_and_indels.cwl

Branch/Commit ID: master

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

Path: workflows/kallisto-demo.cwl

Branch/Commit ID: master

Annotate variants provided in a VCF using SnpEff

https://github.com/cr-ste-justine/chujs-alignment-workflow.git

Path: tools/snpeff-workflow.cwl

Branch/Commit ID: dev

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: downsample_and_recall