diff --git a/.circleci/config.yml b/.circleci/config.yml index 6b799938e..d8040e4b2 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -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 - diff --git a/library/tasks/SplitBamByCellBarcode.wdl b/library/tasks/SplitBamByCellBarcode.wdl index 8733539b1..f8fabd676 100644 --- a/library/tasks/SplitBamByCellBarcode.wdl +++ b/library/tasks/SplitBamByCellBarcode.wdl @@ -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 + # by default request non preemptible machine to make sure the slow cell barcode split step completes Int preemptible = 0 } diff --git a/test/optimus/pr/ValidateOptimus.wdl b/test/optimus/pr/ValidateOptimus.wdl index 78fb04857..5a542f702 100644 --- a/test/optimus/pr/ValidateOptimus.wdl +++ b/test/optimus/pr/ValidateOptimus.wdl @@ -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 diff --git a/test/optimus_mouse/pr/test_inputs.json b/test/optimus_mouse/pr/test_inputs.json index 682330478..9e9e225cd 100644 --- a/test/optimus_mouse/pr/test_inputs.json +++ b/test/optimus_mouse/pr/test_inputs.json @@ -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", diff --git a/test/optimus_snrna/pr/test_inputs.json b/test/optimus_snrna/pr/test_inputs.json index 3b63bda88..23615e31a 100644 --- a/test/optimus_snrna/pr/test_inputs.json +++ b/test/optimus_snrna/pr/test_inputs.json @@ -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" diff --git a/test/options.json b/test/options.json index 720239d58..8383a99c4 100644 --- a/test/options.json +++ b/test/options.json @@ -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 }