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In STAR, it outputs transcriptome based alignment bam files. To sort the bam files and convert the bam files to cram files, it requires transcript.fasta and transcript.fasta.fai file.
So we need to
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Current `Stage_input` subworkflow could process RNAseq data by `study_id` and `analysis_id` input, could not process by `samplesheet` input. This need to be updated.
For RNAseq data, `library_stran…
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Mitchell has been reviewing the ARGO documentation and found several typos that need to be fixed:
1. Remove `to` in "These fields must **to** be coded specifically for ICGC ARGO purposes using the …
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Currently we have ICDO mappings souirced fro NCIT, of the form `ICDO:nnnn/n'
progenetix has more complete mappings
https://github.com/progenetix/ICDOntologies/tree/master/current
TODO: determin…
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Clinical Submissions to RDPC Gateway are returning empty submission data in response
Need to examine submission mutation on clinical and correct the issue
See Slack thread:
https://oicr.slack.com/arc…
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For the `_id` fields in the data model, what are the rules about uniqueness?
CanDIG is assuming that the ids for each schema (Treatment, Donor, Specimen, etc) are unique within that schema for a gi…
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Especially this entry that we really need focusing on ICDO: https://progenetix.org/service-collection/ontologymaps/
@mbaudis
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We need to address the critical security alerts: https://github.com/icgc-argo/files-service/security/dependabot
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Hi, i want to work with the CRAM files from 2 cohorts (PACA-CA and APGI-AU) on the ICGC ARGOS database, I need the genomic information of the HLA region so im trying to get said region via the view…
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Follow up tasks:
- backup cron for song
- icgc.org domain names