VS-361 Add GvsWithdrawSamples wdl #7765
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| cat log_message.txt | sed -e 's/Number of affected rows: //' > rows_updated.txt | ||
| typeset -i rows_updated=$(cat rows_updated.txt) | ||
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| echo "did not update $num_samples rows - only updated $rows_updated" |
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seems like this should only be executed if the counts are mismatched (like the other copy of this on line 82)
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Yeah, that's some leftover debugging code.
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| echo "did not update $num_samples rows - only updated $rows_updated" | ||
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| if [ $num_samples -ne $rows_updated ]; then |
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I really like having this check...I wish there was a cleaner way of doing this with the bq command line tool but if there is I haven't found it... 😞
| String sample_info_table | ||
| Array[String] sample_names | ||
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| # runtime |
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Looking at the other WDLs in this repo this comment appears to be marking inputs that are used in expressions in the runtime section of tasks. Assuming I have that right (which I might not), # runtime would not apply to these two variables.
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Yeah, that's true. I'll remove the comment.
| exit 0 | ||
| fi | ||
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| export GATK_LOCAL_JAR=~{default="/root/gatk.jar" gatk_override} |
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It seems gatk_override isn't actually needed in this WDL and could be removed (there are no GATK invocations here).
| String? service_account_json_path | ||
| } | ||
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| String sample_info_table = "sample_info" |
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Is there a use case that benefits from sample_info_table being a declaration here (and an input in WithdrawSamples) or could its usage just be hardcoded sample_info in WithdrawSamples?
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I wondered about that too - I followed the pattern in another wdl, but I agree that it seems unlikely. I'll remove it as an input.
| runtime { | ||
| docker: "us.gcr.io/broad-gatk/gatk:4.1.7.0" | ||
| memory: "3.75 GB" | ||
| disks: "local-disk " + 10 + " HDD" |
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can this be just one string rather than a concatenation of literals?
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Yeah - would have been a useful pattern if there was a variable for 10
Update to latest gatk docker
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