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Graph Name Retrieved From View
workflow graph module-2.cwl

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

Path: workflows/module-2.cwl

Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf
workflow graph Bismark Methylation - pipeline for BS-Seq data analysis

Sequence reads are first cleaned from adapters and transformed into fully bisulfite-converted forward (C->T) and reverse read (G->A conversion of the forward strand) versions, before they are aligned to similarly converted versions of the genome (also C->T and G->A converted). Sequence reads that produce a unique best alignment from the four alignment processes against the bisulfite genomes (which are running in parallel) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. A read is considered to align uniquely if an alignment has a unique best alignment score (as reported by the AS:i field). If a read produces several alignments with the same number of mismatches or with the same alignment score (AS:i field), a read (or a read-pair) is discarded altogether. On the next step we extract the methylation call for every single C analysed. The position of every single C will be written out to a new output file, depending on its context (CpG, CHG or CHH), whereby methylated Cs will be labelled as forward reads (+), non-methylated Cs as reverse reads (-). The output of the methylation extractor is then transformed into a bedGraph and coverage file. The bedGraph counts output is then used to generate a genome-wide cytosine report which reports the number on every single CpG (optionally every single cytosine) in the genome, irrespective of whether it was covered by any reads or not. As this type of report is informative for cytosines on both strands the output may be fairly large (~46mn CpG positions or >1.2bn total cytosine positions in the human genome).

https://github.com/datirium/workflows.git

Path: workflows/bismark-methylation-se.cwl

Branch/Commit ID: 664de58d95728edbf7d369d894f9037ebe2475fa
workflow graph vcf_to_aliquot_maf_wf.cwl

https://github.com/NCI-GDC/aliquot-maf-cwl.git

Path: vcf-to-aliquot-maf/vcf_to_aliquot_maf_wf.cwl

Branch/Commit ID: 9aedc3fb22a3f5b9146bc5e9a393085050f90c95
workflow graph gp_makeblastdb

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: c009eeba7379efbbd37b8d5013a83f161f06939b
workflow graph protein_extract

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

Path: progs/protein_extract.cwl

Branch/Commit ID: c009eeba7379efbbd37b8d5013a83f161f06939b
workflow graph umi duplex alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_duplex.cwl

Branch/Commit ID: 2e298960837739717ec2928a99c5d811183012e6
workflow graph step-valuefrom3-wf_v1_1.cwl

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

Path: testdata/step-valuefrom3-wf_v1_1.cwl

Branch/Commit ID: e78db9870cb744fe36674f43b3223c688e9989e1
workflow graph SetArrayElementCoordinates

Transform array element coordinates into the coordinate system required by the simulation pipeline (i.e., CORSIKA system).

 https://github.com/gammasim/workflows.git

Path: workflows/SetArrayElementCoordinates.cwl

Branch/Commit ID: 84b99c6e475ad104cdd714d8588ff49805763420
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: 9c0b1497c467393e1a54735575043dced73e95c4
workflow graph count-lines10-wf.cwl

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/count-lines10-wf.cwl

Branch/Commit ID: 62ae25772a8e98b6591554882daa3f3758079fca