msk-access / cwl-commandlinetools

Central location for CWL CommandLineTools
https://cmo-ci.gitbook.io/command-line-tools-cwl/
GNU Affero General Public License v3.0
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Write CWL and Docker for fastp #49

Closed rhshah closed 4 years ago

rhshah commented 4 years ago

Tool: https://github.com/OpenGene/fastp Version: v0.20.1

Example Command:

fastp \
    -i /path/to/fastq/file \
    -o /path/to/output/fastq/file \
    -I /path/to/fastq/file \
    -O /path/to/output/fastq/file \
    --adapter_sequence GATCGGAAGAGC \
    --adapter_sequence_r2 AGATCGGAAGAGC \
    --length_required 25 \
    -j {{sample_name}}.report.json \
    --html {{sample_name}}.report.html
murphycj2 commented 4 years ago

@aef- I added an example command in the description that is likely to be similar to how we will use the tool in the pipeline

rhshah commented 4 years ago

Thank you @murphycj2 and @aef- just a note don't set anything as default based on the above command. Just make sure all the options that we are going to use are covered in CWL.