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icgc-argo / argo-meta

This repo is used to record metadata for testing workflows
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Prepare SONG payloads for THCA-SA WXS data #23

Closed hknahal closed 3 years ago

hknahal commented 3 years ago

Prepare SONG payloads for recently EGA->Collab transferred data (https://github.com/icgc-argo/ega-file-transfer/blob/master/ega_xml/v20200915/THCA-SA/THCA-SA_WXS_Audit_ICGC28.tsv). This dataset consists of 101 donors with whole exome data in Collaboratory (see data in Portal here). Once payloads are generated, they can imported into intermediate-song.

hknahal commented 3 years ago

SONG payloads generated for 100 whole exome donors from ICGC THCA-SA project (in ARGO this is the PTC-SA program). One donor's data (DO234137) is not ready to be imported (normal file: https://github.com/icgc-argo/argo-meta/tree/master/icgc_song_payloads/PTC-SA/WXS/not_imported_batch2) because the tumour file could not be transferred from EGA. I will attempt to re-download the tumour file from EGA and once completed, the tumour/normal pair will be imported later.

hknahal commented 3 years ago

@joneubank The following SONG payloads are ready to be imported to intermediate-song: https://github.com/icgc-argo/argo-meta/tree/master/icgc_song_payloads/PTC-SA/WXS/batch2 The ARGO project code is PTC-SA.