Docpatch #5047
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Docpatch #5047
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Codecov Report
@@ Coverage Diff @@
## master #5047 +/- ##
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+ Coverage 86.379% 86.633% +0.254%
- Complexity 28681 29218 +537
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Files 1785 1810 +25
Lines 132742 135251 +2509
Branches 14773 15000 +227
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+ Hits 114661 117172 +2511
+ Misses 12747 12680 -67
- Partials 5334 5399 +65
|
cmnbroad
requested changes
Aug 27, 2018
| @@ -86,6 +86,7 @@ | |||
| * -V data/gvcfs/father.g.vcf.gz \ | |||
| * -V data/gvcfs/son.g.vcf.gz \ | |||
| * --genomicsdb-workspace-path my_database \ | |||
| * --TMP-DIR=path/to/other/tmp \ | |||
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We recently changed the name of this argument totmp-dir, so the doc here and below should be changed to reflect the new name. Also, I'd suggest using an example path that includes the word large, to reinforce the reason for specifying this:
--tmp-dir=path/to/large/tmp \
| @@ -117,6 +119,7 @@ | |||
| * <li>At least one interval must be provided</li> | |||
| * <li>Input GVCFs cannot contain multiple entries for a single genomic position</li> | |||
| * <li>The --genomicsdb-workspace-path must point to a non-existent or empty directory.</li> | |||
| * <li>GenomicsDBImport makes greedy use of /tmp by default, if your /tmp space is limited this will cause errors once /tmp has filled up. This happens quickly if the tool is running many intervals. It is therefore recommended to specify a different `--TMP-DIR`.</li> | |||
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Suggested wording for this:
GenomicsDBImport uses temporary disk storage during import. The amount of temporary storage required can exceed the space available, especially when using a large number of intervals. The command line argument
--temp-dircan be used to specify an alternate temporary storage location with sufficient space
| @@ -70,6 +71,7 @@ | |||
| * programs produce files that they call GVCFs but those lack some important information (accurate genotype likelihoods | |||
| * for every position) that GenotypeGVCFs requires for its operation.</li> | |||
| * <li>Cannot take multiple GVCF files in one command.</li> | |||
| * <li>Reading from a GenomicsDB workspace can fill up /tmp by default, causing confusing errors when scattering across many intervals. It is recommended to specify a `--TMP-DIR` if running this tool in combination with GenomicsDBImport.</li> | |||
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I'd suggest similar wording here as above.
| @@ -61,7 +61,8 @@ | |||
| * gatk --java-options "-Xmx4g" GenotypeGVCFs \ | |||
| * -R Homo_sapiens_assembly38.fasta \ | |||
| * -V gendb://my_database \ | |||
| * -O output.vcf.gz | |||
| * -O output.vcf.gz \ | |||
| * --TMP-DIR=path/to/other/tmp | |||
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Suggesting --TMP-DIR in documentation of GenomicsDBImport and GenotypeGVCFs