Explore Workflows
View already parsed workflows here or click here to add your own
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step_valuefrom5_wf_with_id_v1_0.cwl
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/step_valuefrom5_wf_with_id_v1_0.cwl Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9 |
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scatter-wf3_v1_1.cwl#main
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/scatter-wf3_v1_1.cwl Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9 Packed ID: main |
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timelimit2-wf.cwl
The entire test should take ~24 seconds. Test that the 20 second time limit applies to each step individually (so 1st step has 20 seconds and the 2nd step has 20 seconds). So this 20 second time limit should not cause the workflow to fail. The timing on this test was updated from shorter values to accommodate the startup time of certain container runners, the previous timelimit of 5 seconds was too short, which is why it is now 20 seconds. |
https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/timelimit2-wf.cwl Branch/Commit ID: 7d7986a6e852ca6e3239c96d3a05dd536c76c903 |
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SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination
Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs. |
https://github.com/datirium/workflows.git
Path: tools/soupx-subworkflow.cwl Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16 |
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Generate genome indices for STAR & bowtie
Creates indices for: * [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) * [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) It performs the following steps: 1. `STAR --runMode genomeGenerate` to generate indices, based on [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) and [GTF](http://mblab.wustl.edu/GTF2.html) input files, returns results as an array of files 2. Outputs indices as [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type 3. Separates *chrNameLength.txt* file from Directory output 4. `bowtie-build` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a group of main and secondary files |
https://github.com/datirium/workflows.git
Path: workflows/genome-indices.cwl Branch/Commit ID: cbefc215d8286447620664fb47076ba5d81aa47f |
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Trim Galore 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-end** 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-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 4. 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/trim-rnaseq-se.cwl Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16 |
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scatter-wf3_v1_0.cwl#main
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/scatter-wf3_v1_0.cwl Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9 Packed ID: main |
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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: fa4f172486288a1a9d23864f1d6962d85a453e16 |
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DESeq2 Multi-factor Analysis
DESeq2 Multi-factor Analysis Runs DeSeq2 multi-factor analysis with manual control over major parameters |
https://github.com/datirium/workflows.git
Path: workflows/deseq-multi-factor.cwl Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16 |
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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: fa4f172486288a1a9d23864f1d6962d85a453e16 |
