Explore Workflows

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/samtools_view_sam2bam.cwl

Branch/Commit ID: master

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

Path: tools/5S-from-tablehits.cwl

Branch/Commit ID: master

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: steps/bulk_analysis.cwl

Branch/Commit ID: 44dbe38

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/fgomez02/analysis-workflows.git

Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl

Branch/Commit ID: No_filters_detect_variants

https://github.com/aldbr/dirac-cwl-proto.git

Path: test/workflows/lhcb/lhcbreconstruct.cwl

Branch/Commit ID: main

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

Path: tests/record-in-secondaryFiles-wf.cwl

Branch/Commit ID: main

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

Path: workflows/cmsearch-multimodel.cwl

Branch/Commit ID: f993cad

https://github.com/slottad/pgap.git

Path: wf_pgap.cwl

Branch/Commit ID: master

https://github.com/adamscharlotte/CWL-workflow.git

Path: ProteinInferenceWorkflow.cwl

Branch/Commit ID: master