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common-workflow-library / legacy

Deprecated
https://github.com/common-workflow-library/bio-cwl-tools
Apache License 2.0
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CWL tool wrappers for bwa, bedtools, samtools #5

Closed portah closed 9 years ago

portah commented 9 years ago

This just a first step to describe bedtools genomecov [OPTIONS] -i "file" -g "genome file"

  1. If input file in one of the bed/gff/vcf formats then prefix is -"i" if it is .bam the prefix is "-ibam"
  2. Genome file must be in "chromName""tab""chromSize" format
  3. For the beginning options has to be optional
portah commented 9 years ago

I did an update bedtools-genomecov requires two params input bam file and genome file. All other params are optional. I don't know how to check type of input file (based on extension) and change prefix -i or -ibam. And force to use one of the params if the other is chosen (like --scale requires either -bg or -bga). The only default engine is JsonPointer or I can use JS?

mr-c commented 9 years ago

I think I'll use this PR to setup an autotester using travis. Are these tests resource intensive?

portah commented 9 years ago

No they are not. All of them one threaded and can be done on a laptop or VM

FarahZKhan commented 9 years ago

Hello, below is the list of GATK tools I was thinking to use for the workflow: • Mapping: Map with BWA for Illumina • Mark duplicates: Picard MarkDuplicates • Indel Realignment: RealignerTargetCreator and IndelRealigner • Base Recalibration: BaseRecalibrator • Data compression with Reduce Reads: ReduceReads • Variant Calling: HaplotypeCaller • Variant recalibration: VariantRecalibrator and ApplyRecalibration • Variant Evaluation: VariantEval I am assuming none of the tools are implemented using CWL as yet. What would be the best place to start? Thank you for all the help earlier,