Explore Workflows

https://git.astron.nl/RD/LINC.git

Path: workflows/HBA_calibrator.cwl

Branch/Commit ID: 0c5bd78e3f2d08564f5c9a563bcc8bb7704e6202

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

Path: tests/dynresreq-workflow-tooldefault.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

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

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3

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

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: 54c5074587af001a44eccb4762a4cb25fa24cb3e

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

Path: metadata/advanced-header.cwl

Branch/Commit ID: ce058d892d330125cd03d0a0d5fb3b321cda0be3

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

Path: cwltool/schemas/v1.0/v1.0/count-lines11-wf.cwl

Branch/Commit ID: a858bb4db58ef2df17b4856294ad7904643c5c6e

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/step-valuefrom3-wf.cwl

Branch/Commit ID: 86c46cb397de029e4c91f02cca40fa2b54d22f37

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: f94719e862f86cc88600caf3628faba6c0d05042

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: c5bae2ca862c764911b83d1f15ff6af4e2a0db28

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

Path: tests/scatter-wf2.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf