Explore Workflows

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

Path: testdata/count-lines7-single-source-wf_v1_2.cwl

Branch/Commit ID: 141048ae4b78aa765782bb752be4a1550edc2eea

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: steps/snapanalysis_setup_and_analyze.cwl

Branch/Commit ID: 102d8cb180bb201d6ef054531a84a764a06c8622

Receive parameter update (e.g., by querying an external source like a configuration or calibration database) or by expert input (e.g., by a member of a telescope team or a simulation pipeline expert).

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

Path: workflows/SetParameterFromExternal.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7

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: 261c0232a7a40880f2480b811ed2d7e89c463869

Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.

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

Path: subworkflows/allele-alignreads-se-pe.cwl

Branch/Commit ID: db6abb2735f87614b870fca9990d36ea786cbbce

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

Path: protein_alignment/wf_align_filter.cwl

Branch/Commit ID: 551493f5c24b757a46cd22821a05e6ac6dcceb7f

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

Path: protein_alignment/wf_compart_filter_prosplign.cwl

Branch/Commit ID: 551493f5c24b757a46cd22821a05e6ac6dcceb7f

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

Path: testdata/step_valuefrom5_wf_v1_1.cwl

Branch/Commit ID: 141048ae4b78aa765782bb752be4a1550edc2eea

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

Path: testdata/step-valuefrom2-wf_v1_0.cwl

Branch/Commit ID: 141048ae4b78aa765782bb752be4a1550edc2eea

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

Path: testdata/step-valuefrom3-wf_v1_1.cwl

Branch/Commit ID: 141048ae4b78aa765782bb752be4a1550edc2eea