From 84fb1f876164bc32d9bb3e5af64fd809adaa5660 Mon Sep 17 00:00:00 2001 From: aawdeh Date: Thu, 16 Jan 2025 06:57:58 -0500 Subject: [PATCH 01/14] Run one star instance --- pipelines/skylab/optimus/Optimus.wdl | 69 ++++++++++------------------ tasks/skylab/StarAlign.wdl | 22 ++++----- 2 files changed, 34 insertions(+), 57 deletions(-) diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl index a975931245..f10e180fa5 100644 --- a/pipelines/skylab/optimus/Optimus.wdl +++ b/pipelines/skylab/optimus/Optimus.wdl @@ -166,23 +166,10 @@ workflow Optimus { ubuntu_docker_path = ubuntu_docker_prefix + ubuntu_docker } - call FastqProcessing.FastqProcessing as SplitFastq { - input: - i1_fastq = i1_fastq, - r1_fastq = r1_fastq, - r2_fastq = r2_fastq, - whitelist = whitelist, - chemistry = tenx_chemistry_version, - sample_id = input_id, - read_struct = read_struct, - warp_tools_docker_path = docker_prefix + warp_tools_docker - } - - scatter(idx in range(length(SplitFastq.fastq_R1_output_array))) { - call StarAlign.STARsoloFastq as STARsoloFastq { + call StarAlign.STARsoloFastq as STARsoloFastq { input: - r1_fastq = [SplitFastq.fastq_R1_output_array[idx]], - r2_fastq = [SplitFastq.fastq_R2_output_array[idx]], + r1_fastq = r1_fastq, + r2_fastq = r2_fastq, star_strand_mode = star_strand_mode, white_list = whitelist, tar_star_reference = tar_star_reference, @@ -195,16 +182,9 @@ workflow Optimus { is_slidetags = is_slidetags } } - call Merge.MergeSortBamFiles as MergeBam { - input: - bam_inputs = STARsoloFastq.bam_output, - output_bam_filename = output_bam_basename + ".bam", - sort_order = "coordinate", - picard_cloud_docker_path = docker_prefix + picard_cloud_docker - } call Metrics.CalculateGeneMetrics as GeneMetrics { input: - bam_input = MergeBam.output_bam, + bam_input = STARsoloFastq.output_bam, mt_genes = mt_genes, original_gtf = annotations_gtf, input_id = input_id, @@ -213,7 +193,7 @@ workflow Optimus { call Metrics.CalculateCellMetrics as CellMetrics { input: - bam_input = MergeBam.output_bam, + bam_input = STARsoloFastq.output_bam, mt_genes = mt_genes, original_gtf = annotations_gtf, input_id = input_id, @@ -222,13 +202,13 @@ workflow Optimus { call StarAlign.MergeStarOutput as MergeStarOutputs { input: - barcodes = STARsoloFastq.barcodes, - features = STARsoloFastq.features, - matrix = STARsoloFastq.matrix, - cell_reads = STARsoloFastq.cell_reads, - summary = STARsoloFastq.summary, - align_features = STARsoloFastq.align_features, - umipercell = STARsoloFastq.umipercell, + barcodes = [STARsoloFastq.barcodes], + features = [STARsoloFastq.features], + matrix = [STARsoloFastq.matrix], + cell_reads = [STARsoloFastq.cell_reads], + summary = [STARsoloFastq.summary], + align_features = [STARsoloFastq.align_features], + umipercell = [STARsoloFastq.umipercell], input_id = input_id, counting_mode = counting_mode, star_merge_docker_path = docker_prefix + star_merge_docker, @@ -272,15 +252,15 @@ workflow Optimus { if (count_exons && counting_mode=="sn_rna") { call StarAlign.MergeStarOutput as MergeStarOutputsExons { input: - barcodes = STARsoloFastq.barcodes_sn_rna, - features = STARsoloFastq.features_sn_rna, - matrix = STARsoloFastq.matrix_sn_rna, - cell_reads = STARsoloFastq.cell_reads_sn_rna, + barcodes = [STARsoloFastq.barcodes_sn_rna], + features = [STARsoloFastq.features_sn_rna], + matrix = [STARsoloFastq.matrix_sn_rna], + cell_reads = ]STARsoloFastq.cell_reads_sn_rna], input_id = input_id, counting_mode = "sc_rna", - summary = STARsoloFastq.summary_sn_rna, - align_features = STARsoloFastq.align_features_sn_rna, - umipercell = STARsoloFastq.umipercell_sn_rna, + summary = [STARsoloFastq.summary_sn_rna], + align_features = [STARsoloFastq.align_features_sn_rna], + umipercell = [STARsoloFastq.umipercell_sn_rna], star_merge_docker_path = docker_prefix + star_merge_docker, gex_nhash_id = gex_nhash_id } @@ -351,7 +331,7 @@ workflow Optimus { # version of this pipeline String pipeline_version_out = pipeline_version File genomic_reference_version = ReferenceCheck.genomic_ref_version - File bam = MergeBam.output_bam + File bam = STARsoloFastq.output_bam File matrix = MergeStarOutputs.sparse_counts File matrix_row_index = MergeStarOutputs.row_index File matrix_col_index = MergeStarOutputs.col_index @@ -363,12 +343,11 @@ workflow Optimus { File? mtx_files = MergeStarOutputs.mtx_files File? filtered_mtx_files = MergeStarOutputs.filtered_mtx_files - Array[File?] multimappers_EM_matrix = STARsoloFastq.multimappers_EM_matrix - Array[File?] multimappers_Uniform_matrix = STARsoloFastq.multimappers_Uniform_matrix - Array[File?] multimappers_Rescue_matrix = STARsoloFastq.multimappers_Rescue_matrix - Array[File?] multimappers_PropUnique_matrix = STARsoloFastq.multimappers_PropUnique_matrix + File? multimappers_EM_matrix = STARsoloFastq.multimappers_EM_matrix + File? multimappers_Uniform_matrix = STARsoloFastq.multimappers_Uniform_matrix + File? multimappers_Rescue_matrix = STARsoloFastq.multimappers_Rescue_matrix + File? multimappers_PropUnique_matrix = STARsoloFastq.multimappers_PropUnique_matrix - # h5ad File h5ad_output_file = final_h5ad_output diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl index b2a07a4d0a..cf0b9f3df8 100644 --- a/tasks/skylab/StarAlign.wdl +++ b/tasks/skylab/StarAlign.wdl @@ -227,18 +227,19 @@ task STARsoloFastq { # runtime values String samtools_star_docker_path - Int machine_mem_mb = 64000 - Int cpu = 8 - # by default request non preemptible machine to make sure the slow star alignment step completes - Int preemptible = 3 # if slide_tags true set disk to 1000 otherwise dynamic allocation based on input size # dynamic allocation multiplies input size by 2.2 to account for output bam file + 20% overhead, add size of reference. Boolean is_slidetags - Int disk = if is_slidetags then 1000 else - ceil(size(tar_star_reference, "Gi") * 3) + - ceil(size(r1_fastq, "Gi") * 20) + - ceil(size(r2_fastq, "Gi") * 20) + + # runtime values + String cpu_platform = "Intel Ice Lake" + Int machine_mem_mb = 512000 + Int mem_size = 512 + Int cpu = 128 + Int disk = 2000 + # by default request non preemptible machine to make sure the slow star alignment step completes + Int preemptible = 1 } meta { @@ -340,9 +341,7 @@ task STARsoloFastq { # validate the bam with samtools quickcheck samtools quickcheck -v Aligned.sortedByCoord.out.bam - echo "UMI LEN " $UMILen - touch barcodes_sn_rna.tsv touch features_sn_rna.tsv touch matrix_sn_rna.mtx @@ -351,7 +350,6 @@ task STARsoloFastq { touch Summary_sn_rna.csv touch UMIperCellSorted_sn_rna.txt - if [[ "~{counting_mode}" == "sc_rna" ]] then SoloDirectory="Solo.out/Gene/raw" @@ -425,7 +423,7 @@ task STARsoloFastq { runtime { docker: samtools_star_docker_path - memory: "~{machine_mem_mb} MiB" + memory: "~{mem_size} GiB" disks: "local-disk ~{disk} HDD" disk: disk + " GB" # TES cpu: cpu From 5d469339e7297cdede20364175b44905950ee35e Mon Sep 17 00:00:00 2001 From: aawdeh Date: Thu, 16 Jan 2025 07:22:59 -0500 Subject: [PATCH 02/14] Run one star instance --- pipelines/skylab/optimus/Optimus.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl index f10e180fa5..50f34a1b59 100644 --- a/pipelines/skylab/optimus/Optimus.wdl +++ b/pipelines/skylab/optimus/Optimus.wdl @@ -181,7 +181,7 @@ workflow Optimus { samtools_star_docker_path = docker_prefix + samtools_star, is_slidetags = is_slidetags } - } + call Metrics.CalculateGeneMetrics as GeneMetrics { input: bam_input = STARsoloFastq.output_bam, From 711a02bba07fbada8b82a132137083c93b4d777e Mon Sep 17 00:00:00 2001 From: aawdeh Date: Thu, 16 Jan 2025 08:47:45 -0500 Subject: [PATCH 03/14] Run one star instance --- pipelines/skylab/optimus/Optimus.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl index 50f34a1b59..764df2176d 100644 --- a/pipelines/skylab/optimus/Optimus.wdl +++ b/pipelines/skylab/optimus/Optimus.wdl @@ -255,7 +255,7 @@ workflow Optimus { barcodes = [STARsoloFastq.barcodes_sn_rna], features = [STARsoloFastq.features_sn_rna], matrix = [STARsoloFastq.matrix_sn_rna], - cell_reads = ]STARsoloFastq.cell_reads_sn_rna], + cell_reads = [STARsoloFastq.cell_reads_sn_rna], input_id = input_id, counting_mode = "sc_rna", summary = [STARsoloFastq.summary_sn_rna], From 59265dd7a705125ac8bcf07b1f11601da79f6d0d Mon Sep 17 00:00:00 2001 From: aawdeh Date: Thu, 16 Jan 2025 08:52:41 -0500 Subject: [PATCH 04/14] Run one star instance --- pipelines/skylab/optimus/Optimus.wdl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl index 764df2176d..3a563152c3 100644 --- a/pipelines/skylab/optimus/Optimus.wdl +++ b/pipelines/skylab/optimus/Optimus.wdl @@ -184,7 +184,7 @@ workflow Optimus { call Metrics.CalculateGeneMetrics as GeneMetrics { input: - bam_input = STARsoloFastq.output_bam, + bam_input = STARsoloFastq.bam_output, mt_genes = mt_genes, original_gtf = annotations_gtf, input_id = input_id, @@ -193,7 +193,7 @@ workflow Optimus { call Metrics.CalculateCellMetrics as CellMetrics { input: - bam_input = STARsoloFastq.output_bam, + bam_input = STARsoloFastq.bam_output, mt_genes = mt_genes, original_gtf = annotations_gtf, input_id = input_id, @@ -331,7 +331,7 @@ workflow Optimus { # version of this pipeline String pipeline_version_out = pipeline_version File genomic_reference_version = ReferenceCheck.genomic_ref_version - File bam = STARsoloFastq.output_bam + File bam = STARsoloFastq.bam_output File matrix = MergeStarOutputs.sparse_counts File matrix_row_index = MergeStarOutputs.row_index File matrix_col_index = MergeStarOutputs.col_index From 9ee5d09a55a7f05384266b6c2b55391be41fe820 Mon Sep 17 00:00:00 2001 From: aawdeh Date: Thu, 16 Jan 2025 08:57:48 -0500 Subject: [PATCH 05/14] Run one star instance --- pipelines/skylab/optimus/Optimus.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl index 3a563152c3..867d8ed2eb 100644 --- a/pipelines/skylab/optimus/Optimus.wdl +++ b/pipelines/skylab/optimus/Optimus.wdl @@ -176,7 +176,7 @@ workflow Optimus { chemistry = tenx_chemistry_version, counting_mode = counting_mode, count_exons = count_exons, - output_bam_basename = output_bam_basename + "_" + idx, + output_bam_basename = output_bam_basename, soloMultiMappers = soloMultiMappers, samtools_star_docker_path = docker_prefix + samtools_star, is_slidetags = is_slidetags From 0f180303c529fabf416a08bbd2b2d1c6128b5418 Mon Sep 17 00:00:00 2001 From: aawdeh Date: Thu, 16 Jan 2025 09:31:57 -0500 Subject: [PATCH 06/14] fix --- tasks/skylab/StarAlign.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl index cf0b9f3df8..6a6afc9370 100644 --- a/tasks/skylab/StarAlign.wdl +++ b/tasks/skylab/StarAlign.wdl @@ -233,7 +233,7 @@ task STARsoloFastq { Boolean is_slidetags # runtime values - String cpu_platform = "Intel Ice Lake" + String cpu_platform = "Intel Cascade Lake" Int machine_mem_mb = 512000 Int mem_size = 512 Int cpu = 128 From 4c8e1e7886bf12eab9909eb713781cab82285183 Mon Sep 17 00:00:00 2001 From: aawdeh Date: Thu, 16 Jan 2025 09:39:37 -0500 Subject: [PATCH 07/14] fix --- tasks/skylab/StarAlign.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl index 6a6afc9370..1eedeeeae0 100644 --- a/tasks/skylab/StarAlign.wdl +++ b/tasks/skylab/StarAlign.wdl @@ -234,7 +234,6 @@ task STARsoloFastq { # runtime values String cpu_platform = "Intel Cascade Lake" - Int machine_mem_mb = 512000 Int mem_size = 512 Int cpu = 128 Int disk = 2000 @@ -427,6 +426,7 @@ task STARsoloFastq { disks: "local-disk ~{disk} HDD" disk: disk + " GB" # TES cpu: cpu + cpuPlatform: cpu_platform preemptible: preemptible } From c3c1b975140d3ac2fc901c27d237b32c5d70d632 Mon Sep 17 00:00:00 2001 From: aawdeh Date: Thu, 16 Jan 2025 09:42:28 -0500 Subject: [PATCH 08/14] fix --- tasks/skylab/StarAlign.wdl | 1 + 1 file changed, 1 insertion(+) diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl index 1eedeeeae0..c2f39bde8d 100644 --- a/tasks/skylab/StarAlign.wdl +++ b/tasks/skylab/StarAlign.wdl @@ -235,6 +235,7 @@ task STARsoloFastq { # runtime values String cpu_platform = "Intel Cascade Lake" Int mem_size = 512 + Int machine_mem_mb = 512000 Int cpu = 128 Int disk = 2000 # by default request non preemptible machine to make sure the slow star alignment step completes From a6079c4e6ab405026b05fc71dc8808bae23f37ac Mon Sep 17 00:00:00 2001 From: aawdeh Date: Thu, 16 Jan 2025 10:05:46 -0500 Subject: [PATCH 09/14] fix --- tasks/skylab/StarAlign.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl index c2f39bde8d..4e54bf8c65 100644 --- a/tasks/skylab/StarAlign.wdl +++ b/tasks/skylab/StarAlign.wdl @@ -233,7 +233,7 @@ task STARsoloFastq { Boolean is_slidetags # runtime values - String cpu_platform = "Intel Cascade Lake" + String cpu_platform = "Intel Ice Lake" Int mem_size = 512 Int machine_mem_mb = 512000 Int cpu = 128 @@ -424,7 +424,7 @@ task STARsoloFastq { runtime { docker: samtools_star_docker_path memory: "~{mem_size} GiB" - disks: "local-disk ~{disk} HDD" + disks: "local-disk ~{disk} SSD" disk: disk + " GB" # TES cpu: cpu cpuPlatform: cpu_platform From 3e20a5dc733f0ebf3e9ee978f314ab90dcbddf31 Mon Sep 17 00:00:00 2001 From: aawdeh Date: Thu, 16 Jan 2025 10:19:26 -0500 Subject: [PATCH 10/14] fix --- pipelines/skylab/paired_tag/PairedTag.wdl | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/pipelines/skylab/paired_tag/PairedTag.wdl b/pipelines/skylab/paired_tag/PairedTag.wdl index a31d3c5944..31c3b55790 100644 --- a/pipelines/skylab/paired_tag/PairedTag.wdl +++ b/pipelines/skylab/paired_tag/PairedTag.wdl @@ -176,16 +176,16 @@ workflow PairedTag { File? cell_calls_gex = Optimus.cell_calls File h5ad_output_file_gex = Optimus.h5ad_output_file File? library_metrics = Optimus.library_metrics - Array[File?] multimappers_EM_matrix = Optimus.multimappers_EM_matrix - Array[File?] multimappers_Uniform_matrix = Optimus.multimappers_Uniform_matrix - Array[File?] multimappers_Rescue_matrix = Optimus.multimappers_Rescue_matrix - Array[File?] multimappers_PropUnique_matrix = Optimus.multimappers_PropUnique_matrix + File? multimappers_EM_matrix = Optimus.multimappers_EM_matrix + File? multimappers_Uniform_matrix = Optimus.multimappers_Uniform_matrix + File? multimappers_Rescue_matrix = Optimus.multimappers_Rescue_matrix + File? multimappers_PropUnique_matrix = Optimus.multimappers_PropUnique_matrix File? cell_barcodes_csv = Optimus.cell_barcodes_csv File? checkpoint_file = Optimus.checkpoint_file - Array[File]? h5_array = Optimus.h5_array - Array[File]? html_report_array = Optimus.html_report_array + File? h5_array = Optimus.h5_array + File? html_report_array = Optimus.html_report_array File? log = Optimus.log - Array[File]? metrics_csv_array = Optimus.metrics_csv_array + File? metrics_csv_array = Optimus.metrics_csv_array String? output_directory = Optimus.output_directory File? summary_pdf = Optimus.summary_pdf } From 093428aef313eb459f48d5bd329d09efc757d493 Mon Sep 17 00:00:00 2001 From: aawdeh Date: Thu, 16 Jan 2025 10:26:10 -0500 Subject: [PATCH 11/14] Parameterize soloCBmatchWLtype --- tasks/skylab/StarAlign.wdl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl index 4e54bf8c65..aba985d40e 100644 --- a/tasks/skylab/StarAlign.wdl +++ b/tasks/skylab/StarAlign.wdl @@ -224,6 +224,7 @@ task STARsoloFastq { String output_bam_basename Boolean? count_exons String? soloMultiMappers + String soloCBmatchWLtype = "1MM_multi" #"1MM_multi_Nbase_pseudocounts" # runtime values String samtools_star_docker_path @@ -328,7 +329,7 @@ task STARsoloFastq { --soloFeatures $COUNTING_MODE \ --clipAdapterType CellRanger4 \ --outFilterScoreMin 30 \ - --soloCBmatchWLtype 1MM_multi \ + --soloCBmatchWLtype ~{soloCBmatchWLtype} \ --soloUMIdedup 1MM_CR \ --outSAMtype BAM SortedByCoordinate \ --outSAMattributes UB UR UY CR CB CY NH GX GN sF cN \ From 2e363e95555e9ae6226fe7853960c4ea6c608fb9 Mon Sep 17 00:00:00 2001 From: aawdeh Date: Thu, 16 Jan 2025 10:38:15 -0500 Subject: [PATCH 12/14] fix --- pipelines/skylab/multiome/Multiome.wdl | 8 ++++---- pipelines/skylab/paired_tag/PairedTag.wdl | 6 +++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl index 1553513fd7..adac4d3e88 100644 --- a/pipelines/skylab/multiome/Multiome.wdl +++ b/pipelines/skylab/multiome/Multiome.wdl @@ -160,10 +160,10 @@ workflow Multiome { File gene_metrics_gex = Optimus.gene_metrics File? cell_calls_gex = Optimus.cell_calls File h5ad_output_file_gex = JoinBarcodes.gex_h5ad_file - Array[File?] multimappers_EM_matrix = Optimus.multimappers_EM_matrix - Array[File?] multimappers_Uniform_matrix = Optimus.multimappers_Uniform_matrix - Array[File?] multimappers_Rescue_matrix = Optimus.multimappers_Rescue_matrix - Array[File?] multimappers_PropUnique_matrix = Optimus.multimappers_PropUnique_matrix + File? multimappers_EM_matrix = Optimus.multimappers_EM_matrix + File? multimappers_Uniform_matrix = Optimus.multimappers_Uniform_matrix + File? multimappers_Rescue_matrix = Optimus.multimappers_Rescue_matrix + File? multimappers_PropUnique_matrix = Optimus.multimappers_PropUnique_matrix File? gex_aligner_metrics = Optimus.aligner_metrics File? library_metrics = Optimus.library_metrics File? mtx_files = Optimus.mtx_files diff --git a/pipelines/skylab/paired_tag/PairedTag.wdl b/pipelines/skylab/paired_tag/PairedTag.wdl index 31c3b55790..2c1bb928f4 100644 --- a/pipelines/skylab/paired_tag/PairedTag.wdl +++ b/pipelines/skylab/paired_tag/PairedTag.wdl @@ -182,10 +182,10 @@ workflow PairedTag { File? multimappers_PropUnique_matrix = Optimus.multimappers_PropUnique_matrix File? cell_barcodes_csv = Optimus.cell_barcodes_csv File? checkpoint_file = Optimus.checkpoint_file - File? h5_array = Optimus.h5_array - File? html_report_array = Optimus.html_report_array + Array[File]? h5_array = Optimus.h5_array + Array[File]? html_report_array = Optimus.html_report_array File? log = Optimus.log - File? metrics_csv_array = Optimus.metrics_csv_array + Array[File]? metrics_csv_array = Optimus.metrics_csv_array String? output_directory = Optimus.output_directory File? summary_pdf = Optimus.summary_pdf } From 25b2a886b6fe5d61de117b83f8c15a8a46d16e43 Mon Sep 17 00:00:00 2001 From: aawdeh Date: Mon, 20 Jan 2025 09:35:27 -0500 Subject: [PATCH 13/14] increase ram sort limit --- tasks/skylab/StarAlign.wdl | 1 + 1 file changed, 1 insertion(+) diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl index aba985d40e..1f0e372df4 100644 --- a/tasks/skylab/StarAlign.wdl +++ b/tasks/skylab/StarAlign.wdl @@ -334,6 +334,7 @@ task STARsoloFastq { --outSAMtype BAM SortedByCoordinate \ --outSAMattributes UB UR UY CR CB CY NH GX GN sF cN \ --soloBarcodeReadLength 0 \ + --limitBAMsortRAM 33195969137 \ --soloCellReadStats Standard \ ~{"--soloMultiMappers " + soloMultiMappers} \ --soloUMIfiltering MultiGeneUMI_CR \ From 8a911764e3b93a60eae195cfe523a26d5879a982 Mon Sep 17 00:00:00 2001 From: aawdeh Date: Mon, 20 Jan 2025 09:44:42 -0500 Subject: [PATCH 14/14] increase ram sort limit --- tasks/skylab/StarAlign.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl index 1f0e372df4..c497220eb7 100644 --- a/tasks/skylab/StarAlign.wdl +++ b/tasks/skylab/StarAlign.wdl @@ -316,7 +316,7 @@ task STARsoloFastq { echo Error: unknown counting mode: "$counting_mode". Should be either sn_rna or sc_rna. exit 1; fi - + # RAM limit 33195969137 STAR \ --soloType Droplet \ --soloStrand ~{star_strand_mode} \