Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph basic.cwl

https://github.com/screx/cwl-tutorial.git

Path: cl-tools/workflow/basic.cwl

Branch/Commit ID: master
workflow graph rRNA_selection.cwl

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

Path: tools/rRNA_selection.cwl

Branch/Commit ID: 8e196ab
workflow graph orgaquant_wf.cwl

https://github.com/AlexanderSenf/orgaquant.git

Path: orgaquant_wf.cwl

Branch/Commit ID: 1.1
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: rnaseq/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: toil_compatibility
workflow graph tRNA_selection.cwl

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

Path: tools/tRNA_selection.cwl

Branch/Commit ID: e1b0fce
workflow graph facets-suite-workflow.cwl

Workflow for running the facets suite workflow on a single tumor normal pair Includes handling of errors in case execution fails for the sample pair

https://github.com/mskcc/pluto-cwl.git

Path: cwl/facets-suite-workflow.cwl

Branch/Commit ID: master
workflow graph kfdrc_cram_reheader_wf.cwl

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

Path: workflows/kfdrc_cram_reheader_wf.cwl

Branch/Commit ID: dev
workflow graph rRNA_selection.cwl

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

Path: tools/rRNA_selection.cwl

Branch/Commit ID: c1f8b22
workflow graph standard_bam_to_collapsed_qc.cwl

This is a workflow to go from standard bams to collapsed bams and QC results.

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

Path: workflows/subworkflows/standard_bam_to_collapsed_qc.cwl

Branch/Commit ID: master
workflow graph 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

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

Path: workflows/qiime-workflow.cwl

Branch/Commit ID: 8e196ab