Vcf2maf #101
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Vcf2maf #101
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Adding the CWL & Readme for Mosdepth
Feature/add mosdepth ## most recent commit for mosdepth_0.3.3.cwl includes the following changes: ## * Includes additional input parameters --flag and --mapq used to filter out low quality reads * Reformatted output files structure in cwl in outputs section as there are multiple output files ### Testing: cwl was tested with both cwltool and toil-cwl-runner on ika: ### * command used to run job nohup toil-cwl-runner --singularity --outdir $PWD/test_mosdepth_0.3.3_access mosdepth_0.3.3.cwl test_mosdepth_0.3.3.yml & * input yaml can be found here at /work/bergerm1/bergerlab/charalk/projects/mosdepth/test_mosdepth_0.3.3.yml * output files can be found in folder /work/bergerm1/bergerlab/charalk/projects/mosdepth/test_mosdepth_0.3.3_access * log file can be found at /work/bergerm1/bergerlab/charalk/projects/mosdepth/nohup.out ### Job completed successfully and the correct number of non-empty mosdepth files were created. ###
Feature/vardict
commit
updated namespace and descrip
Added octopus
updated cwl
updated github url
Feature/add octopus
making a practice cwl script for running delly tools.
✔️ Dockerfile ✔️ CWL file ✔️ README Co-Authored-By: Eric Buehler <[email protected]>
adding memory requirements to athena cwls
✔️ bumping to version that creates unique Id for hotspots table
✔️ bumping to version that creates unique Id for hotspots table using `sample:chromsome:start_position:end_position:ref_allele:alt_allele1:alt_allele2`
✔️ adding version with calculation for library yield
bumping cci_utils
✔️ defensive programming
bumping cci_update
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@rhshah custom-enst option parameter is updated from string to File