Workflow: pdx-pl.cwl

Fetched 2021-11-29 15:22:08 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
adapters File
read2 File
read1 File

Steps

ID Runs Label Doc
platypus
../tools/src/tools/platypus.cwl (CommandLineTool)
sort-human
../tools/src/tools/samtools-sort.cwl (CommandLineTool)
xenomapping
../tools/src/tools/xenomapper.cwl (CommandLineTool)
gridss-tabix
../tools/src/tools/tabix.cwl (CommandLineTool)
index-human
../tools/src/tools/samtools-index.cwl (CommandLineTool)
gridss-bgzip
../tools/src/tools/bgzip.cwl (CommandLineTool)
rename_reads2_trimmed_paired
../tools/src/tools/rename-file.cwl (CommandLineTool)
platypus-tabix
../tools/src/tools/tabix.cwl (CommandLineTool)
platypus-bgzip
../tools/src/tools/bgzip.cwl (CommandLineTool)
trim
../tools/src/tools/trimmomatic.cwl (CommandLineTool)

Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters. These adapters can pose a real problem depending on the library preparation and downstream application. There are two major modes of the program: Paired end mode and Single end mode. The paired end mode will maintain correspondence of read pairs and also use the additional information contained in paired reads to better find adapter or PCR primer fragments introduced by the library preparation process. Trimmomatic works with FASTQ files (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used).

rename_reads1_trimmed
../tools/src/tools/rename-file.cwl (CommandLineTool)
convert-human
../tools/src/tools/samtools-view.cwl (CommandLineTool)
align-to-mouse
../tools/src/tools/bowtie2.cwl (CommandLineTool)

bowtie2.cwl is developed for CWL consortium

gridss-human
../tools/src/tools/gridss-callvariants.cwl (CommandLineTool)
align-to-human
../tools/src/tools/bowtie2.cwl (CommandLineTool)

bowtie2.cwl is developed for CWL consortium

Outputs

ID Type Label Doc
gridss-tabix-output File
platypus-tabix-output File
rename_reads2_trimmed_paired_file File (Optional)
primary_multi File (Optional)
primary_specific File (Optional)
human-compress File
gridss-vcf-work-dir Directory
reads2_trimmed_unpaired_file File (Optional)
unassigned File (Optional)
gridss-bam-work-dir Directory
secondary_specific File (Optional)
rename_reads1_trimmed_file File
unresolved File (Optional)
human-sorted File
human-index File
mouse-aligned File
reads1_trimmed_unpaired_file File (Optional)
trim-logs File
secondary_multi File (Optional)
human-aligned File
Permalink: https://w3id.org/cwl/view/git/4bf9858ea46ed81165357e1b15575c581cb5c181/src/pdx-pl.cwl