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increased the HDD to 3500 GB, from 500 GB originally, to speed-up the SplitBamByCellBarcode step #358

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increased the HDD to 3500 GB, from 500 GB originally, to speed-up the SplitBamByCellBarcode step #358

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5d2efac
increased the HDD to 3500 GB, from 500 GB originally, and updated the…
kishorikonwar Jul 28, 2020
0366569
minor formatting
kishorikonwar Jul 29, 2020
bdf25a5
Merge branch 'master' of github.com:HumanCellAtlas/skylab into kmk-sp…
kishorikonwar Jul 29, 2020
b0ab763
fixed pr error
kishorikonwar Jul 30, 2020
b40d146
fixed pr for optimus_mouse
kishorikonwar Jul 31, 2020
991cf4e
fixed validation results
kishorikonwar Aug 3, 2020
7736f0c
fixed tests
kishorikonwar Aug 3, 2020
4d09c7b
test set to read from cache true
kishorikonwar Aug 3, 2020
ff57e22
run limited tests
kishorikonwar Aug 3, 2020
083a3e1
matrix
kishorikonwar Aug 4, 2020
b459f84
matrix
kishorikonwar Aug 4, 2020
a5a4cc4
matrix
kishorikonwar Aug 4, 2020
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15 changes: 7 additions & 8 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -188,17 +188,16 @@ workflows:
version: 2
test_all:
jobs:
- test_optimus
- test_optimus_snrna
# - test_optimus
# - test_optimus_snrna
# - test_emptyDropsWrapper
- test_optimus_mouse
- test_smartseq2
- test_smartseq2_single_end
- test_npz2rds
- test_snap_atac
- test_sc_atac
- test_bulk_rna
- test_optimus_v3
# - test_npz2rds
# - test_snap_atac
# - test_sc_atac
# - test_bulk_rna
# - test_optimus_v3
- test_smartseq2_multisample
- test_smartseq2_multisample_single_end

5 changes: 3 additions & 2 deletions library/tasks/SplitBamByCellBarcode.wdl
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Expand Up @@ -6,13 +6,14 @@ task SplitBamByCellBarcode {
Float size_in_mb = 1024.0

# runtime values
String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.5"
String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.9"

Int machine_mem_mb = 15258
Int cpu = 16

# we can calculate disk size for arrays of input files in WDL 1.0
Int disk = 500
Int disk = 3500
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should we calculate this based on input size rather than just always getting a ton of disk?


# by default request non preemptible machine to make sure the slow cell barcode split step completes
Int preemptible = 0
}
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2 changes: 1 addition & 1 deletion test/optimus/pr/ValidateOptimus.wdl
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Expand Up @@ -265,7 +265,7 @@ task GenerateReport {
fail=false

echo Bam Validation: ~{bam_validation_result}
if [ "~{bam_validation_result}" == "FAIL"]; then
if [ "~{bam_validation_result}" == "FAIL" ]; then
fail=true
fi

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2 changes: 1 addition & 1 deletion test/optimus_mouse/pr/test_inputs.json
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@@ -1,5 +1,5 @@
{
"TestOptimusPR.expected_bam_hash": "8ff09ba3b0df8ac5a4c8276cde239b72",
"TestOptimusPR.expected_bam_hash": "d832a4fa8362c61ae1fc8096d85690fd",
"TestOptimusPR.expected_matrix_hash": "79d0e000e9e707e16fce1ecc1559cd5d",
"TestOptimusPR.expected_cell_metric_hash": "627baa8511cea26b33f12e4f8021fc5d",
"TestOptimusPR.expected_gene_metric_hash": "30ad387acf91764a937c1adf3bc8bb66",
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6 changes: 3 additions & 3 deletions test/optimus_snrna/pr/test_inputs.json
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@@ -1,9 +1,9 @@
{
"TestOptimusPR.expected_bam_hash": "77bb8a250b56d913a0d75c63f67c17da",
"TestOptimusPR.reference_matrix": "gs://hca-dcp-sc-pipelines-test-data/optimus-test-data/referenceMatrix_snrna.rds",
"TestOptimusPR.expected_cell_metric_hash": "8df13b6298f1baccf95d18b4f50b7089",
"TestOptimusPR.expected_gene_metric_hash": "71fd4a40176b4e3728d6a3ac4317764b",
"TestOptimusPR.expected_loom_file_checksum": "6cd0d7f1cb4c92a215d7b21ff50dc72d",
"TestOptimusPR.expected_cell_metric_hash": "fee06b8f0dfae528ef13d06283214190",
"TestOptimusPR.expected_gene_metric_hash": "2ef1173b79a899eab55f28785533f4f0",
"TestOptimusPR.expected_loom_file_checksum": "3dd004e0ef286bbf193945df6dbe7739",
"TestOptimusPR.r1_fastq": [
"gs://hca-dcp-sc-pipelines-test-data/smallDatasets/chemistry_X10_V2/nuclei_900/nuclei_900_S1_L001_R1_001.filtered.fastq.gz",
"gs://hca-dcp-sc-pipelines-test-data/smallDatasets/chemistry_X10_V2/nuclei_900/nuclei_900_S1_L002_R1_001.filtered.fastq.gz"
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2 changes: 1 addition & 1 deletion test/options.json
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@@ -1,5 +1,5 @@
{
"monitoring_script": "gs://hca-dcp-mint-test-data/accessories/monitoring/cellranger/monitoring.sh",
"read_from_cache": true,
"write_to_cache": true
"write_to_cache": false
}