Closed amandaraud closed 6 months ago
NGI workflow set-up: https://docs.google.com/spreadsheets/d/1JKTgZmP6pnPfjUJtSt6gL-yTqmHN6PJ8Yp0joG3U_nY/edit#gid=183845737
Comments and requests from LF: https://docs.google.com/document/d/1OQBI0tdQVhBlzRhnlmuUfw4YbKi6uEfgXjpJAuHX-MY/edit
(tell me if you need access to view them)
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy process-to-sample -sudf 'Received at' -pudf 'Date arrived at Clinical Genomics'"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf check check-artifact-udfs -i -au 'Concentration' -au 'Amount (ng)'"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf calculate calculate-amount-ng-fmol -n 'DNA Fragmentation (ONT)' --concentration-udf 'Concentration' --volume-udf 'Volume (ul)' --size-udf 'Size (bp)' --preset-volume 50"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf calculate ont-aliquot-volume -n 'DNA Fragmentation (ONT)' --concentration-udf 'Input Concentration (ng/ul)' --size-udf 'Size (bp)' --volume-udf 'Sample Volume (ul)' --buffer-udf 'Volume H2O (ul)' --total-volume-udf 'Total Volume (ul)'"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy artifact-to-artifact --sample-artifact -au 'Input Size (bp)' -sau 'Size (bp)' -au 'Input Amount (ng)' -sau 'Amount (ng)' -au 'Volume (ul)' -sau 'Volume (ul)' -sau 'Concentration' -au 'Input Concentration (ng/ul)'"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf calculate ont-aliquot-volume -n 'DNA Fragmentation (ONT)' -n 'DNA Size Selection (ONT)' --concentration-udf 'Input Concentration (ng/ul)' --size-udf 'Size (bp)' --volume-udf 'Sample Volume (ul)' --buffer-udf 'Volume H2O (ul)' --total-volume-udf 'Total Volume (ul)' "
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf calculate calculate-amount-ng-fmol -n 'DNA Fragmentation (ONT)' -n 'DNA Size Selection (ONT)' --concentration-udf 'Concentration' --volume-udf 'Volume (ul)' --size-udf 'Size (bp)' --preset-volume 37"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy artifact-to-artifact -n 'DNA Fragmentation (ONT)' -au 'Input Size (bp)' -sau 'Size (bp)' -au 'Input Amount (ng)' -sau 'Amount (ng)' -au 'Volume (ul)' -sau 'Volume (ul)' -sau 'Concentration' -au 'Input Concentration (ng/ul)'"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf calculate ont-aliquot-volume -n 'DNA Fragmentation (ONT)' -n 'DNA Size Selection (ONT)' --concentration-udf 'Concentration' --size-udf 'Size (bp)' --volume-udf 'Sample Volume (ul)' --buffer-udf 'Volume H2O (ul)' --total-volume-udf 'Total Volume (ul)'"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy artifact-to-artifact --sample-artifact -au 'Concentration' -sau 'Concentration' -au 'Amount (ng)' -sau 'Amount (ng)' && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy artifact-to-artifact -n 'DNA Fragmentation (ONT)' -n 'DNA Size Selection (ONT)' -au 'Concentration' -sau 'Concentration' -au 'Amount (ng)' -sau 'Amount (ng)' --ignore-fail"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf set updated-sample-volume -sa && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf set updated-sample-volume -n 'DNA Fragmentation (ONT)' -pudf 'Total Volume (ul)' --subtract-volume 5 --ignore-fail && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf set updated-sample-volume -n 'DNA Size Selection (ONT)' -pudf 'Total Volume (ul)' --subtract-volume 13 --ignore-fail"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf calculate calculate-amount-ng-fmol -n 'DNA Fragmentation (ONT)' -n 'DNA Size Selection (ONT)' --concentration-udf 'Concentration (ng/ul)' --volume-udf 'Volume (ul)' --size-udf 'Size (bp)' --preset-volume 60"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy artifact-to-artifact --process-types 'Aliquot Samples for ONT Prep' -au 'Input Amount (ng)' -sau 'Amount (ng)'"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf set updated-sample-volume -n 'Aliquot Samples for ONT Prep' -pudf 'Total Volume (ul)'"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy artifact-to-artifact --process-types 'Aliquot Samples for ONT Prep' -au 'Input Amount (ng)' -sau 'Amount (ng)'"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf calculate calculate-amount-ng-fmol -n 'DNA Fragmentation (ONT)' -n 'DNA Size Selection (ONT)' --concentration-udf 'Concentration' --volume-udf 'Volume (ul)' --size-udf 'Size (bp)' --preset-volume 24 -i"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf calculate ont-aliquot-volume -n 'DNA Fragmentation (ONT)' -n 'DNA Size Selection (ONT)' --concentration-udf 'Concentration' --size-udf 'Size (bp)' --volume-udf 'Sample Volume (ul)' --buffer-udf 'Volume Buffer (ul)' --total-volume-udf 'Loading Volume (ul)' --amount-fmol-udf 'Loading Amount (fmol)'"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy artifact-to-artifact -au 'Concentration' -au 'Amount (fmol)' -n 'ONT Adapter Ligation'"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy container-to-artifact -n 'ONT Adapter Ligation' --well-udf 'Input Container Well' --container-name-udf 'Input Container Name'"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} files create-ont-sample-sheet -f {compoundOutputFileLuid1}"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf set set-ont-sequencing-settings"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf calculate ont-available-sequencing-reload"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf calculate ont-aliquot-volume -n 'DNA Fragmentation (ONT)' -n 'DNA Size Selection (ONT)' --concentration-udf 'Concentration' --size-udf 'Size (bp)' --volume-udf 'Sample Volume (ul)' --buffer-udf 'Buffer Volume (ul)' --amount-fmol-udf 'Reload Amount (fmol)' --total-volume-udf 'Reload Volume (ul)' -m"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (input.hasValue( ::Rerun:: ) && input.::Rerun:: == true) { nextStep = ::REMOVE:: } else { nextStep = ::ADVANCE:: }' -log {compoundOutputFileLuid1}"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid4} -p {processLuid} files parse-ont-report --root-path /home/gls/nanopore_data"
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} move rerun-samples -u 'Rerun' -n 'ONT Adapter Ligation' -w 2152 -s 7487 -i"
Fantastic 🥇
We are going to start sequencing samples with ONT for the 100 genomes project, which is planned to start in December. Luckily enough, NGI have been running ONT samples for some time, and already have a LIMS workflow set up for it:
A meeting is planned in order to discuss how much of their implementation can be used by us, and what changes that are needed.
The current deadline for having this in production is around the 5-10th of December, but this might change depending on how the lab and IT implementations progress.