Explore Workflows

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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.cwl

Branch/Commit ID: b141f7e73005227d6d02fa03a47151836dd4109b

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

Path: tests/count-lines3-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

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

Path: tests/count-lines7-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

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

Path: tests/count-lines8-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

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

Path: tests/count-lines1-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

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

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869

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

Path: cwltool/schemas/v1.0/v1.0/count-lines12-wf.cwl

Branch/Commit ID: 6d2998467fada81e5024c1f8594ae167514cb290

https://github.com/lanl/BEE.git

Path: examples/cat-grep-tar/workflow.cwl

Branch/Commit ID: cd51dc29a5c74773cd82a704e3cf26126ad43138

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 49732e54e2fe2eafd2f82df3c482c73e642f6d64

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: 707ebcd2173889604459c5f4ffb55173c508abb3