Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph conflict.cwl#main

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

Path: tests/wf/conflict.cwl

Branch/Commit ID: 1b5633876aabd4cb57ef3f1fe91c853f3ee82e46

Packed ID: main
workflow graph Trim Galore RNA-Seq pipeline paired-end

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow must be used with paired-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 2 (after running STAR) 5. Generate BigWig file using sorted BAM file 6. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

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

Path: workflows/trim-rnaseq-pe.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph wf.cwl

https://github.com/ResearchObject/runcrate.git

Path: cwl/multisource/wf.cwl

Branch/Commit ID: 376f6b2c6332a4742d4512d6e1fb785a2f8b7285
workflow graph count-lines7-wf_v1_1.cwl

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

Path: testdata/count-lines7-wf_v1_1.cwl

Branch/Commit ID: 5759b4275906e6cfe13912c8426de2a2237cb4b0
workflow graph pipeline_v2.cwl#openoil_pipeline

Animation of an oil spill with openoil

 https://github.com/ILIAD-ocean-twin/application_package.git

Path: openoil/pipeline_v2.cwl

Branch/Commit ID: 2f678aa688683e20169abaaec9166b4a32403523

Packed ID: openoil_pipeline
workflow graph Single-Cell ATAC-Seq Genome Coverage

Single-Cell ATAC-Seq Genome Coverage Generates genome coverage tracks from chromatin accessibility data of selected cells

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

Path: workflows/sc-atac-coverage.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph alignment-pair.cwl

https://github.com/mskcc/argos-cwl.git

Path: modules/pair/alignment-pair.cwl

Branch/Commit ID: 0b9721d7d512352c7f80b27f42b3192a585ed5f6
workflow graph Single-Cell RNA-Seq Trajectory Analysis

Single-Cell RNA-Seq Trajectory Analysis Infers developmental trajectories and pseudotime from cells clustered by similarity of gene expression data.

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

Path: workflows/sc-rna-trajectory.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph scatter-wf2_v1_2.cwl

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

Path: testdata/scatter-wf2_v1_2.cwl

Branch/Commit ID: 5759b4275906e6cfe13912c8426de2a2237cb4b0
workflow graph Interval overlapping alignments counts

Interval overlapping alignments counts ====================================== Reports the count of alignments from multiple samples that overlap specific intervals.

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

Path: workflows/bedtools-multicov.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20