dreichlab / adna-workflow Goto Github PK
View Code? Open in Web Editor NEWWorkflow for processing Illumina sequencing runs for ancient human DNA
License: Other
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adna-workflow's Issues
Unknown cromwell error
org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "UC_WORKFLOW_METADATA_SUMMARY_ENTRY_WEU"
at cromwell.database.slick.SlickDatabase.$anonfun$runActionInternal$1(SlickDatabase.scala:228)
at scala.concurrent.Future$.$anonfun$apply$1(Future.scala:678)
at scala.concurrent.impl.Promise$Transformation.run(Promise.scala:467)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Check deduplication barcode error
For errors in barcodes, make sure that deduplication does not result in overrepresentation of error sequences..
Workflow running even without the correct imports.zip
Workflow running fine even without the correct input wdls in the imports.zip
sample merges have incorrect read group PU
The PU field for sample merges appears to have the library instead of the platform unit (flowcell).
clipping option for MT fasta
Provide a clipping option for mt_fasta.py
versions is incorrectly call-cached
The versions file is call-cached and should not be.
Clean BAM files
https://broadinstitute.github.io/picard/command-line-overview.html#CleanSam
This should eliminate the problems with >0 mapping quality for unmapped reads that cause issues for Picard.
demultiplex by lane, then merge
Processing NovaSeq flowcells is very slow, due to the bottleneck of demultiplexing, which is currently linear for the whole flowcell. This can be improved by demultiplexing each lane separately, then merging the resulting bams.
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