Explore Workflows

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

Graph Name Retrieved From View
workflow graph RNA-Seq pipeline single-read

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-read** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file 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/rnaseq-se.cwl

Branch/Commit ID: 29bf638904709cfbf10908adcd51ba4886ace94a
workflow graph pindel parallel workflow

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

Path: definitions/subworkflows/pindel.cwl

Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 76a9637a06e2102645eae29aff10b6f7185892a5
workflow graph umi per-lane alignment subworkflow

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

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: 31602b94b34ff55876147c7299e1bec47e8d1a31
workflow graph HS Metrics workflow

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0
workflow graph 1st-workflow.cwl

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: 6c86caa0571fd186d90a6600e0bb405596d4a5e0
workflow graph count-lines4-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines4-wf.cwl

Branch/Commit ID: 4700fbee9a5a3271eef8bc9ee595619d0720431b
workflow graph RNA-Seq pipeline paired-end stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific pair-end** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with the pair-end strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `samtools sort` to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file 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/rnaseq-pe-dutp-mitochondrial.cwl

Branch/Commit ID: ee66d03be8a7fd61367db40c37a973ff55ece4da
workflow graph Run pindel on provided region

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

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: 31602b94b34ff55876147c7299e1bec47e8d1a31
workflow graph directory.cwl

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: bffea7fd5e864c5221c13a815d00d0a2fad178cc