Explore Workflows
View already parsed workflows here or click here to add your own
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wf_exec_paleocar.cwl
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https://github.com/idaks/cwl_modeling.git
Path: yw_cwl_modeling/yw_cwl_parser_old/Examples/exec_paleocar/wf_exec_paleocar.cwl Branch/Commit ID: master |
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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 |
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Water bodies detection based on NDWI and the otsu threshold
Water bodies detection based on NDWI and otsu threshold applied to a single Sentinel-2 COG STAC item |
https://github.com/eoap/quickwin.git
Path: cwl-workflow/app-water-body-cloud-native.cwl Branch/Commit ID: main Packed ID: main |
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preprocessAndCluster.cwl
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https://github.com/Epigenomics-Screw/Screw.git
Path: cwl/preprocessAndCluster.cwl Branch/Commit ID: scatter |
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Unaligned BAM to BQSR and VCF
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https://github.com/genome/cancer-genomics-workflow.git
Path: unaligned_bam_to_bqsr/workflow_no_dup_marking.cwl Branch/Commit ID: toil_compatibility |
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bams2gvcf.woBQSR_female_chrX_wXTR.multisapmles.cwl
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https://github.com/ddbj/human-reseq.git
Path: Workflows/bams2gvcf.woBQSR_female_chrX_wXTR.multisapmles.cwl Branch/Commit ID: master |
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Functional analyis of sequences that match the 16S SSU
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: workflows/16S_taxonomic_analysis.cwl Branch/Commit ID: 0cd2d70 |
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chksum_seqval_wf_paired_fq.cwl
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https://github.com/cancerit/workflow-seq-import.git
Path: cwls/chksum_seqval_wf_paired_fq.cwl Branch/Commit ID: 0.2.2 |
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cmsearch-multimodel.cwl
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: workflows/cmsearch-multimodel.cwl Branch/Commit ID: 43d2fb8 |
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rnaseq-alignment-quantification
This workflow retrieve SRA fastqc data and execute QC, alignment and quantification from TPMCalculator |
https://github.com/ncbi/cwl-ngs-workflows-cbb.git
Path: workflows/RNA-Seq/rnaseq-quantification-qc.cwl Branch/Commit ID: master |
