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microbiomedata / mg_annotation

Metagenome Annotation Workflow
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added support for triplets #9

Open Michal-Babins opened 2 years ago

Michal-Babins commented 2 years ago

Added support in generate_objects.py to be able to take FIle | Description | Name to run code as such:

python generate_objects.py --type "nmdc:ReadQCAnalysisActivity" --id ${informed_by} \
             --name "Read QC Activity for ${proj}" --part ${proj} \
             --start ${start} --end $end \
             --resource '${resource}' --url ${url_root}${proj}/qa/ --giturl ${git_url} \
             --extra stats.json \
             --inputs  Ecoli_10x-int.fastq.gz \
             --outputs \
             ${qadir}/nmdc_mga0rgxp26_filtered.fastq.gz "Reads QC result fastq (clean data)" "Filtered Sequencing Read"\
             ${qadir}/nmdc_mga0rgxp26_filterStats.txt "Reads QC summary statistics" "QC Statistics"