broadinstitute · nikellepetrillo · Jan 16, 2024 · Nov 16, 2023 · Nov 21, 2023 · Nov 29, 2023
diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
@@ -1,3 +1,8 @@
+# 3.0.5
+2024-01-11 (Date of Last Commit)
+
+* Added the --soloMultiMappers flag as an optional input to the StarSoloFastq task in the StarAlign.wdl
+
 # 3.0.4
 2024-01-05 (Date of Last Commit)
 

diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
@@ -6,7 +6,7 @@ import "../../../tasks/skylab/H5adUtils.wdl" as H5adUtils
 import "https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.0/wdl/cellbender_remove_background.wdl" as CellBender
 
 workflow Multiome {
-    String pipeline_version = "3.0.4"
+    String pipeline_version = "3.0.5"
 
     input {
         String input_id
@@ -27,6 +27,7 @@ workflow Multiome {
         String star_strand_mode = "Forward"
         Boolean count_exons = false
         File gex_whitelist = "gs://gcp-public-data--broad-references/RNA/resources/arc-v1/737K-arc-v1_gex.txt"
+        String? soloMultiMappers
 
         # ATAC inputs
         # Array of input fastq files
@@ -67,6 +68,7 @@ workflow Multiome {
             ignore_r1_read_length = ignore_r1_read_length,
             star_strand_mode = star_strand_mode,
             count_exons = count_exons,
+            soloMultiMappers = soloMultiMappers
     }
 
     # Call the ATAC workflow
@@ -134,6 +136,11 @@ 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] soloMultiMappers = Optimus.soloMultiMappers
+        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
 
         # cellbender outputs
         File? cell_barcodes_csv = CellBender.cell_csv

diff --git a/pipelines/skylab/multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json b/pipelines/skylab/multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json
@@ -23,5 +23,6 @@
   "Multiome.run_cellbender":"false",
   "Multiome.Atac.BWAPairedEndAlignment.cpu_platform":"Intel Cascade Lake",
   "Multiome.Atac.BWAPairedEndAlignment.mem_size":"64",
-  "Multiome.Atac.BWAPairedEndAlignment.nthreads":"16"
+  "Multiome.Atac.BWAPairedEndAlignment.nthreads":"16",
+  "Multiome.soloMultiMappers":"Uniform"
 }
diff --git a/pipelines/skylab/optimus/Optimus.changelog.md b/pipelines/skylab/optimus/Optimus.changelog.md
@@ -1,3 +1,7 @@
+# 6.3.4
+2024-01-11 (Date of Last Commit)
+* Added the --soloMultiMappers flag as an optional input to the StarSoloFastq task in the StarAlign.wdl
+
 # 6.3.3
 2024-01-05 (Date of Last Commit)
 * Modified the STARsoloFastq task in the StarAlign.wdl so STARsolo can run different types of alignments in a single STARsolo command depending on the counting_mode

diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
@@ -31,6 +31,7 @@ workflow Optimus {
     File annotations_gtf
     File ref_genome_fasta
     File? mt_genes
+    String? soloMultiMappers
 
     # Chemistry options include: 2 or 3
     Int tenx_chemistry_version
@@ -64,7 +65,7 @@ workflow Optimus {
 
   # version of this pipeline
 
-  String pipeline_version = "6.3.3"
+  String pipeline_version = "6.3.4"
 
   # this is used to scatter matched [r1_fastq, r2_fastq, i1_fastq] arrays
   Array[Int] indices = range(length(r1_fastq))
@@ -131,7 +132,8 @@ 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 + "_" + idx,
+        soloMultiMappers = soloMultiMappers
     }
   }
   call Merge.MergeSortBamFiles as MergeBam {
@@ -237,6 +239,12 @@ workflow Optimus {
     File gene_metrics = GeneMetrics.gene_metrics
     File? cell_calls = RunEmptyDrops.empty_drops_result
     File? aligner_metrics = MergeStarOutputs.cell_reads_out
+    Array[File] soloMultiMappers = STARsoloFastq.matrix_sn_rna
+    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
+
     # h5ad
     File h5ad_output_file = final_h5ad_output
   }

diff --git a/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json b/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json
@@ -16,5 +16,6 @@
   "Optimus.tenx_chemistry_version": "3",
   "Optimus.annotations_gtf": "gs://gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf",
   "Optimus.star_strand_mode": "Forward",
-  "Optimus.ref_genome_fasta": "gs://gcp-public-data--broad-references/hg38/v0/GRCh38.primary_assembly.genome.fa"
+  "Optimus.ref_genome_fasta": "gs://gcp-public-data--broad-references/hg38/v0/GRCh38.primary_assembly.genome.fa",
+  "Optimus.soloMultiMappers": "EM"
 }
diff --git a/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_example.json b/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_example.json
@@ -28,5 +28,6 @@
   "Optimus.tenx_chemistry_version": "2",
   "Optimus.star_strand_mode": "Unstranded",
   "Optimus.annotations_gtf": "gs://gcp-public-data--broad-references/GRCm39/star/v2_7_10a/modified_vM32.annotation.gtf",
-  "Optimus.ref_genome_fasta": "gs://gcp-public-data--broad-references/GRCm39/GRCm39.primary_assembly.genome.fa.gz"
+  "Optimus.ref_genome_fasta": "gs://gcp-public-data--broad-references/GRCm39/GRCm39.primary_assembly.genome.fa.gz",
+  "Optimus.soloMultiMappers": "EM"
 }
diff --git a/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_snRNA_example.json b/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_snRNA_example.json
@@ -26,5 +26,6 @@
   "Optimus.annotations_gtf": "gs://gcp-public-data--broad-references/GRCm39/star/v2_7_10a/modified_vM32.annotation.gtf",
   "Optimus.ref_genome_fasta": "gs://gcp-public-data--broad-references/GRCm39/GRCm39.primary_assembly.genome.fa.gz",
   "Optimus.counting_mode": "sn_rna",
-  "Optimus.count_exons": true
+  "Optimus.count_exons": true,
+  "Optimus.soloMultiMappers": "EM"
 }
diff --git a/pipelines/skylab/paired_tag/PairedTag.changelog.md b/pipelines/skylab/paired_tag/PairedTag.changelog.md
@@ -1,3 +1,7 @@
+# 0.0.4
+2024-01-11 (Date of Last Commit)
+* Added the --soloMultiMappers flag as an optional input to the StarSoloFastq task in the StarAlign.wdl
+
 # 0.0.3
 2024-01-05 (Date of Last Commit)
 

diff --git a/pipelines/skylab/paired_tag/PairedTag.wdl b/pipelines/skylab/paired_tag/PairedTag.wdl
@@ -5,7 +5,7 @@ import "../../../pipelines/skylab/optimus/Optimus.wdl" as optimus
 import "../../../tasks/skylab/H5adUtils.wdl" as H5adUtils
 import "../../../tasks/skylab/PairedTagUtils.wdl" as Demultiplexing
 workflow PairedTag {
-    String pipeline_version = "0.0.3"
+    String pipeline_version = "0.0.4"
 
     input {
         String input_id

diff --git a/pipelines/skylab/slideseq/SlideSeq.changelog.md b/pipelines/skylab/slideseq/SlideSeq.changelog.md
@@ -1,3 +1,7 @@
+# 2.1.5
+2024-01-11 (Date of Last Commit)
+* Added the --soloMultiMappers flag as an optional input to the StarSoloFastq task in the StarAlign.wdl; this does affect the SlideSeq workflow
+
 # 2.1.4
 2024-01-05 (Date of Last Commit)
 * Modified the STARsoloFastq task in the StarAlign.wdl so STARsolo can run different types of alignments in a single STARsolo command depending on the counting_mode; this does affect the SlideSeq workflow

diff --git a/pipelines/skylab/slideseq/SlideSeq.wdl b/pipelines/skylab/slideseq/SlideSeq.wdl
@@ -23,7 +23,7 @@ import "../../../tasks/skylab/MergeSortBam.wdl" as Merge
 
 workflow SlideSeq {
 
-    String pipeline_version = "2.1.4"
+    String pipeline_version = "2.1.5"
 
     input {
         Array[File] r1_fastq

diff --git a/...tseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md b/...tseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
@@ -1,3 +1,7 @@
+# 1.2.28
+2024-01-11 (Date of Last Commit)
+* Added the --soloMultiMappers flag as an optional input to the StarSoloFastq task in the StarAlign.wdl; this does affect the MultiSampleSmartSeq2SingleNucleus workflow
+
 # 1.2.27
 2024-01-05 (Date of Last Commit)
 * Modified the STARsoloFastq task in the StarAlign.wdl so STARsolo can run different types of alignments in a single STARsolo command depending on the counting_mode; this does affect the MultiSampleSmartSeq2SingleNucleus workflow

diff --git a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl
@@ -40,7 +40,7 @@ workflow MultiSampleSmartSeq2SingleNucleus {
       String? input_id_metadata_field
   }
   # Version of this pipeline
-  String pipeline_version = "1.2.27"
+  String pipeline_version = "1.2.28"
 
   if (false) {
      String? none = "None"

diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl
@@ -223,6 +223,7 @@ task STARsoloFastq {
     String counting_mode # when counting_mode = sn_rna, runs Gene and GeneFullEx50pAS in single alignments
     String output_bam_basename
     Boolean? count_exons
+    String? soloMultiMappers
 
     # runtime values
     String docker = "us.gcr.io/broad-gotc-prod/star:1.0.1-2.7.11a-1692706072"
@@ -308,7 +309,8 @@ task STARsoloFastq {
         --outSAMtype BAM SortedByCoordinate \
         --outSAMattributes UB UR UY CR CB CY NH GX GN sF \
         --soloBarcodeReadLength 0 \
-        --soloCellReadStats Standard
+        --soloCellReadStats Standard \
+        ~{"--soloMultiMappers " + soloMultiMappers}
     elif [[ "~{counting_mode}" == "sn_rna" ]]
     then
         ## single nuclei
@@ -333,7 +335,8 @@ task STARsoloFastq {
             --outSAMtype BAM SortedByCoordinate \
             --outSAMattributes UB UR UY CR CB CY NH GX GN sF \
             --soloBarcodeReadLength 0 \
-            --soloCellReadStats Standard
+            --soloCellReadStats Standard \
+            ~{"--soloMultiMappers " + soloMultiMappers}
         else
             COUNTING_MODE="GeneFull_Ex50pAS Gene"
             echo "Running in ~{counting_mode} mode. Count_exons is true and the Star parameter --soloFeatures will be set to $COUNTING_MODE"
@@ -354,16 +357,14 @@ task STARsoloFastq {
             --outSAMtype BAM SortedByCoordinate \
             --outSAMattributes UB UR UY CR CB CY NH GX GN sF \
             --soloBarcodeReadLength 0 \
-            --soloCellReadStats Standard
+            --soloCellReadStats Standard \
+            ~{"--soloMultiMappers " + soloMultiMappers}
         fi
     else
         echo Error: unknown counting mode: "$counting_mode". Should be either sn_rna or sc_rna.
         exit 1;
     fi
 
-
-
-
     echo "UMI LEN " $UMILen
 
     touch barcodes_sn_rna.tsv
@@ -377,9 +378,12 @@ task STARsoloFastq {
 
     if [[ "~{counting_mode}" == "sc_rna" ]]
     then
+      SoloDirectory="Solo.out/Gene/raw"
+      echo "SoloDirectory is $SoloDirectory"
+      find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{}  echo mv {} /cromwell_root/
+      find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/
       mv "Solo.out/Gene/raw/barcodes.tsv" barcodes.tsv
       mv "Solo.out/Gene/raw/features.tsv" features.tsv
-      mv "Solo.out/Gene/raw/matrix.mtx"   matrix.mtx
       mv "Solo.out/Gene/CellReads.stats" CellReads.stats
       mv "Solo.out/Gene/Features.stats" Features.stats
       mv "Solo.out/Gene/Summary.csv" Summary.csv
@@ -388,24 +392,34 @@ task STARsoloFastq {
     then
       if [[ "~{count_exons}" == "false" ]]
       then
+        SoloDirectory="Solo.out/GeneFull_Ex50pAS/raw"
+        echo "SoloDirectory is $SoloDirectory"
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{}  echo mv {} /cromwell_root/
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/
         mv "Solo.out/GeneFull_Ex50pAS/raw/barcodes.tsv" barcodes.tsv
         mv "Solo.out/GeneFull_Ex50pAS/raw/features.tsv" features.tsv
-        mv "Solo.out/GeneFull_Ex50pAS/raw/matrix.mtx"   matrix.mtx
         mv "Solo.out/GeneFull_Ex50pAS/CellReads.stats" CellReads.stats
         mv "Solo.out/GeneFull_Ex50pAS/Features.stats" Features.stats
         mv "Solo.out/GeneFull_Ex50pAS/Summary.csv" Summary.csv
         mv "Solo.out/GeneFull_Ex50pAS/UMIperCellSorted.txt" UMIperCellSorted.txt
       else
+        SoloDirectory="Solo.out/GeneFull_Ex50pAS/raw"
+        echo "SoloDirectory is $SoloDirectory"
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} echo mv {} /cromwell_root/
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/
+        SoloDirectory="Solo.out/Gene/raw"
+        echo "SoloDirectory is $SoloDirectory"
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} sh -c 'new_name="$(basename {} .mtx)_sn_rna.mtx";  echo mv {} "/cromwell_root/$new_name"'
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} sh -c 'new_name="$(basename {} .mtx)_sn_rna.mtx"; mv {} "/cromwell_root/$new_name"'
         mv "Solo.out/GeneFull_Ex50pAS/raw/barcodes.tsv" barcodes.tsv
         mv "Solo.out/GeneFull_Ex50pAS/raw/features.tsv" features.tsv
-        mv "Solo.out/GeneFull_Ex50pAS/raw/matrix.mtx"   matrix.mtx
         mv "Solo.out/GeneFull_Ex50pAS/CellReads.stats" CellReads.stats
         mv "Solo.out/GeneFull_Ex50pAS/Features.stats" Features.stats
         mv "Solo.out/GeneFull_Ex50pAS/Summary.csv" Summary.csv
         mv "Solo.out/GeneFull_Ex50pAS/UMIperCellSorted.txt" UMIperCellSorted.txt
         mv "Solo.out/Gene/raw/barcodes.tsv"     barcodes_sn_rna.tsv
         mv "Solo.out/Gene/raw/features.tsv"     features_sn_rna.tsv
-        mv "Solo.out/Gene/raw/matrix.mtx"       matrix_sn_rna.mtx
+        #mv "Solo.out/Gene/raw/matrix.mtx"       matrix_sn_rna.mtx
         mv "Solo.out/Gene/CellReads.stats" CellReads_sn_rna.stats
         mv "Solo.out/Gene/Features.stats" Features_sn_rna.stats
         mv "Solo.out/Gene/Summary.csv" Summary_sn_rna.csv
@@ -445,6 +459,10 @@ task STARsoloFastq {
     File align_features_sn_rna = "Features_sn_rna.stats"
     File summary_sn_rna = "Summary_sn_rna.csv"
     File umipercell_sn_rna = "UMIperCellSorted_sn_rna.txt"
+    File? multimappers_EM_matrix = "UniqueAndMult-EM.mtx"
+    File? multimappers_Uniform_matrix = "UniqueAndMult-Uniform.mtx"
+    File? multimappers_Rescue_matrix = "UniqueAndMult-Rescue.mtx"
+    File? multimappers_PropUnique_matrix = "UniqueAndMult-PropUnique.mtx"
   }
 }
 

diff --git a/verification/test-wdls/TestMultiome.wdl b/verification/test-wdls/TestMultiome.wdl
@@ -27,6 +27,7 @@ workflow TestMultiome {
       String star_strand_mode = "Forward"
       Boolean count_exons = false
       File gex_whitelist = "gs://broad-gotc-test-storage/Multiome/input/737K-arc-v1_gex.txt"
+      String? soloMultiMappers
 
       # ATAC inputs
       # Array of input fastq files
@@ -84,7 +85,8 @@ workflow TestMultiome {
         adapter_seq_read3 = adapter_seq_read3,
         chrom_sizes = chrom_sizes,
         atac_whitelist = atac_whitelist,
-        run_cellbender = run_cellbender
+        run_cellbender = run_cellbender,
+        soloMultiMappers = soloMultiMappers
 
     }
 

diff --git a/verification/test-wdls/TestOptimus.wdl b/verification/test-wdls/TestOptimus.wdl
@@ -26,6 +26,7 @@ workflow TestOptimus {
     File annotations_gtf
     File ref_genome_fasta
     File? mt_genes
+    String? soloMultiMappers
 
     # Chemistry options include: 2 or 3
     Int tenx_chemistry_version = 2
@@ -84,7 +85,8 @@ workflow TestOptimus {
       force_no_check             = force_no_check,
       star_strand_mode           = star_strand_mode,
       count_exons                = count_exons,
-      ignore_r1_read_length      = ignore_r1_read_length
+      ignore_r1_read_length      = ignore_r1_read_length,
+      soloMultiMappers           = soloMultiMappers
   }
 
   # Collect all of the pipeling output into single Array

diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md
@@ -7,7 +7,7 @@ slug: /Pipelines/Multiome_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [Multiome v3.0.4](https://github.com/broadinstitute/warp/releases) | January, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact the [WARP Pipeline Development team](mailto:warp-pipelines-help@broadinstitute.org) |
+| [Multiome v3.0.5](https://github.com/broadinstitute/warp/releases) | January, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact the [WARP Pipeline Development team](mailto:warp-pipelines-help@broadinstitute.org) |
 
 ![Multiome_diagram](./multiome_diagram.png)
 
@@ -70,6 +70,7 @@ Multiome can be deployed using [Cromwell](https://cromwell.readthedocs.io/en/sta
 | star_strand_mode | Optional string for the Optimus (GEX) pipeline for performing STARsolo alignment on forward stranded, reverse stranded, or unstranded data; default is "Forward". | String |
 | count_exons | Optional boolean for the Optimus (GEX) pipeline indicating if the workflow should calculate exon counts **when in single-nucleus (sn_rna) mode**; if "true" in sc_rna mode, the workflow will return an error; default is "false". | Boolean |
 | gex_whitelist | Optional file containing the list of valid barcodes for 10x multiome GEX data; default is "gs://gcp-public-data--broad-references/RNA/resources/arc-v1/737K-arc-v1_gex.txt". | File |
+| soloMultiMappers | Optional string describing whether or not the Optimus (GEX) pipeline should run STARsolo with the `--soloMultiMappers` flag. | String |
 | atac_r1_fastq | Array of read 1 paired-end FASTQ files representing a single 10x multiome ATAC library. | Array[File] |
 | atac_r2_fastq | Array of barcodes FASTQ files representing a single 10x multiome ATAC library. | Array[File] |
 | atac_r3_fastq | Array of read 2 paired-end FASTQ files representing a single 10x multiome ATAC library. | Array[File] |
@@ -114,6 +115,11 @@ The Multiome workflow calls two WARP subworkflows, one external subworkflow (opt
 | gene_metrics_gex | `<input_id>_gex.gene_metrics.csv.gz` | CSV file containing the per-gene metrics. |
 | cell_calls_gex | `<input_id>_gex.emptyDrops` | TSV file containing the EmptyDrops results when the Optimus workflow is run in sc_rna mode. |
 | h5ad_output_file_gex | `<input_id>_gex.h5ad` | h5ad (Anndata) file containing the raw cell-by-gene count matrix, gene metrics, cell metrics, and global attributes. Also contains equivalent ATAC barcode for each gene expression barcode in the `atac_barcodes` column of the `h5ad.obs` property. See the [Optimus Count Matrix Overview](../Optimus_Pipeline/Loom_schema.md) for more details. |
+| soloMultiMappers |
+| multimappers_EM_matrix |
+| multimappers_Uniform_matrix |
+| multimappers_Rescue_matrix |
+| multimappers_PropUnique_matrix |
 | cell_barcodes_csv | `<cell_csv>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [GitHub repository](https://github.com/broadinstitute/CellBender/tree/master) for more information. |
 | checkpoint_file | `<ckpt_file>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [GitHub repository](https://github.com/broadinstitute/CellBender/tree/master) for more information. |
 | h5_array | `<h5_array>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [GitHub repository](https://github.com/broadinstitute/CellBender/tree/master) for more information. |