Explore Workflows

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d

https://github.com/Marco-Salvi/cwl-ro-crate.git

Path: ST520112.cwl

Branch/Commit ID: main

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

Path: tests/scatter-valuefrom-wf5.cwl

Branch/Commit ID: e62f99dd79d6cb9c157cceb458f74200da84f6e9

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/dev/ultra-opt/workflows/kfdrc_bwamem_subwf.cwl

Branch/Commit ID: 9fc3770230e1bd8495f5e6a18665bd21e7c6fafd

https://github.com/bcbio/bcbio_validation_workflows.git

Path: wes-agha-test/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl

Branch/Commit ID: master

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 51724b44c96e5fd849ae55b752865b80bc47d66c

https://github.com/kevinsayers/cwl_rnatoy.git

Path: rnatoy.cwl

Branch/Commit ID: master

https://github.com/4dn-dcic/pipelines-cwl.git

Path: cwl_awsem_v1/hi-c-processing-bam.cwl

Branch/Commit ID: dev2

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/common-workflow-language/cwl-v1.2.git

Path: tests/conditionals/cond-wf-003.1_nojs.cwl

Branch/Commit ID: e62f99dd79d6cb9c157cceb458f74200da84f6e9