Explore Workflows

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 4b8d11048f1047140b337a2cac6503d80a22d683

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

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: 69c0f25d08cfa02d8bfaa85ce5d70dd14cc52e3f

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

Path: definitions/pipelines/aml_trio_cle_gathered.cwl

Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb

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

Path: tests/scatter-valuefrom-inputs-wf1.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b

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

Path: v1.0/v1.0/scatter-wf4.cwl

Branch/Commit ID: 17695244222b0301b37cb749fe4a8d89622cd1ad

Packed ID: main

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-pe.cwl

Branch/Commit ID: 822a07cd6937faa4be377b0cac8780f52c817faf

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

Path: tests/wf/secret_wf.cwl

Branch/Commit ID: efd59864c24d97e6d0d1d273025d3ef9003fa44d

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: ffab5424bb8b5905aecf6f8e2e6387da7f3df562

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: 86fbeb95ef85111f3b4c6bc2bba8f06cef64e157

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

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

Path: tests/wf/directory.cwl

Branch/Commit ID: baa668bc96ade54607465d21bc6cfa15c9bff13c