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V15 subset files (2/2) #555

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merged 12 commits into from
Mar 1, 2024
Merged

V15 subset files (2/2) #555

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5b0f9d5
update tcga file names in data files description
jharenza Mar 1, 2024
5ddb77f
v15 testing data
jharenza Mar 1, 2024
1aa6948
Update data-files-description.md
jharenza Mar 1, 2024
1e6b524
update runs to v4 to use node20 since node16 is deprecated
jharenza Mar 1, 2024
5f30179
test - free disk space before each run
jharenza Mar 1, 2024
1810065
try some more removal steps
jharenza Mar 1, 2024
dd25a4b
remove old docker images if present
jharenza Mar 1, 2024
ed1784e
remove rm packages bit
jharenza Mar 1, 2024
ccc25fa
remove tumor only from GA for mut sigs
jharenza Mar 1, 2024
c6fa632
update CI param
jharenza Mar 1, 2024
3355b78
remove semicolon
jharenza Mar 1, 2024
c4993a3
Merge pull request #556 from d3b-center/v15-ga-update
jharenza Mar 1, 2024
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Binary file modified analyses/create-subset-files/biospecimen_ids_for_subset.RDS
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2 changes: 1 addition & 1 deletion analyses/create-subset-files/run_create_subset_files.sh
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Expand Up @@ -8,7 +8,7 @@ set -o pipefail

# Set defaults for release and biospecimen file name
BIOSPECIMEN_FILE=${BIOSPECIMEN_FILE:-biospecimen_ids_for_subset.RDS}
RELEASE=${RELEASE:-v14}
RELEASE=${RELEASE:-v15}
NUM_MATCHED=${NUM_MATCHED:-15}

# This option controls whether or not the two larger MAF files are skipped as
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3 changes: 2 additions & 1 deletion doc/data-files-description.md
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Expand Up @@ -40,7 +40,8 @@ This document contains information about all data files associated with this pro
|`fusion-putative-oncogenic.tsv` | Analysis file | [`fusion_filtering`](https://github.com/d3b-center/OpenPedCan-analysis/tree/master/analyses/fusion_filtering) | Filtered and prioritized fusions
|`gene-counts-rsem-expected_count-collapsed.rds` | Analysis file | PBTA+GMKF+TARGET [`collapse-rnaseq`](https://github.com/d3b-center/OpenPedCan-analysis/tree/dev/analyses/collapse-rnaseq) | Gene expression - RSEM expected_count for each samples collapsed to gene symbol (gene-level)
|`gene-expression-rsem-tpm-collapsed.rds` | Analysis file | PBTA+GMKF+TARGET [`collapse-rnaseq`](https://github.com/d3b-center/OpenPedCan-analysis/tree/dev/analyses/collapse-rnaseq) | Gene expression - RSEM TPM for each samples collapsed to gene symbol (gene-level)
|`tcga-gene-expression-rsem-tpm-collapsed.rds` | Modified reference file | TCGA samples lifted from GENCODE v27 to v39 | Gene expression - RSEM TPM for each samples collapsed to gene symbol (gene-level)
|`tcga_gene-counts-rsem-expected_count-collapsed.rds` | Modified reference file | TCGA samples lifted from GENCODE v27 to v39 | Gene expression - RSEM counts for each samples collapsed to gene symbol (gene-level)
|`tcga_gene-expression-rsem-tpm-collapsed.rds` | Modified reference file | TCGA samples lifted from GENCODE v27 to v39 | Gene expression - RSEM TPM for each samples collapsed to gene symbol (gene-level)
|`gtex-gene-expression-rsem-tpm-collapsed.rds` | Modified reference file | GTEX v8 release lifted to GENCODE v39 | Gene expression - RSEM TPM for each samples collapsed to gene symbol (gene-level)
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|`gtex_gene-counts-rsem-expected_count-collapsed.rds` | Modified reference file | GTEX v8 release lifted to GENCODE v39 | Gene expression - RSEM counts for each samples collapsed to gene symbol (gene-level)
|`WGS.hg38.lancet.300bp_padded.bed` | Reference Target/Baits File | [SNV and INDEL calling](https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/master/content/03.methods.md#snv-and-indel-calling) | WGS.hg38.lancet.unpadded.bed file with each region padded by 300 bp
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