Explore Workflows

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

Graph Name Retrieved From View
workflow graph freebayes.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/variant_calling/freebayes.cwl

Branch/Commit ID: master
workflow graph fastq_contamination_cleanup

This workflow detect and remove contamination from a DNA fasta file

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/Contamination/fastq-contamination-cleanup.cwl

Branch/Commit ID: master
workflow graph Add snv and indel bam-readcount files to a vcf

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

Path: definitions/subworkflows/vcf_readcount_annotator.cwl

Branch/Commit ID: downsample_and_recall
workflow graph collate_unique_SSU_headers.cwl

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

Path: tools/collate_unique_SSU_headers.cwl

Branch/Commit ID: ca6ca613
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf.cwl

Branch/Commit ID: downsample_and_recall
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: downsample_and_recall
workflow graph Salmon quantification, FASTQ -> H5AD count matrix

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: steps/salmon-quantification.cwl

Branch/Commit ID: 1550b3e
workflow graph qiime2 importing data

Obtaining and importing data from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

 https://github.com/Duke-GCB/bespin-cwl.git

Path: packed/qiime2-step1-import-demux.cwl

Branch/Commit ID: qiime2-workflow-paired

Packed ID: qiime2-01-import-data.cwl
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: 3168316
workflow graph spiel.cwl

https://github.com/gijzelaerr/spiel.git

Path: spiel.cwl

Branch/Commit ID: master