From 4d8b21ccfed5d88c5a36194a329912c34e35cffa Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Thu, 16 Nov 2023 10:35:32 -0500
Subject: [PATCH 01/23] add summary task

---
 beta-pipelines/skylab/m3c/CondensedSnm3C.wdl | 123 +++++++++++++------
 1 file changed, 87 insertions(+), 36 deletions(-)

diff --git a/beta-pipelines/skylab/m3c/CondensedSnm3C.wdl b/beta-pipelines/skylab/m3c/CondensedSnm3C.wdl
index d53d32a6e1..98dd357584 100644
--- a/beta-pipelines/skylab/m3c/CondensedSnm3C.wdl
+++ b/beta-pipelines/skylab/m3c/CondensedSnm3C.wdl
@@ -87,20 +87,20 @@ workflow WDLized_snm3C {
           chrom_size_path = chromosome_sizes
    }
 
-   # call summary {
-   #     input:
-   #         trimmed_stats = Sort_and_trim_r1_and_r2.trim_stats,
-   #         hisat3n_stats = Hisat_3n_pair_end_mapping_dna_mode.hisat3n_stats,
-   #         r1_hisat3n_stats = hisat_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name.r1_hisat3n_stats,
-   #         r2_hisat3n_stats = hisat_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name.r2_hisat3n_stats,
-   #         dedup_stats = dedup_unique_bam_and_index_unique_bam.dedup_stats,
-   #         chromatin_contact_stats = call_chromatin_contacts.chromatin_contact_stats,
-   #         allc_uniq_reads_stats = unique_reads_allc.allc_uniq_reads_stats,
-   #         unique_reads_cgn_extraction_tbi = unique_reads_cgn_extraction.unique_reads_cgn_extraction_tbi
-   # }
+    call summary {
+        input:
+            trimmed_stats = Sort_and_trim_r1_and_r2.trim_stats_tar,
+            hisat3n_stats = Hisat_3n_pair_end_mapping_dna_mode.hisat3n_paired_end_stats_tar,
+            r1_hisat3n_stats = Hisat_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name.hisat3n_dna_split_reads_summary_R1_tar,
+            r2_hisat3n_stats = Hisat_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name.hisat3n_dna_split_reads_summary_R2_tar,
+            dedup_stats = dedup_unique_bam_and_index_unique_bam.dedup_stats_tar,
+            chromatin_contact_stats = call_chromatin_contacts.chromatin_contact_stats,
+            allc_uniq_reads_stats = unique_reads_allc.allc_uniq_reads_stats,
+            unique_reads_cgn_extraction_tbi = unique_reads_cgn_extraction.output_tbi_tar
+    }
 
     output {
-        #File MappingSummary = summary.MappingSummary
+        File MappingSummary = summary.mapping_summary
         #File allcFiles = unique_reads_allc.
         #File allc_CGNFiles = unique_reads_cgn_extraction.
         #File UniqueAlign_cell_parser_picard_dedup = dedup_unique_bam_and_index_unique_bam.dedup_stats
@@ -545,6 +545,11 @@ task Hisat_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name
          --threads 11 | samtools view -b -q 10 -o "${sample_id}.hisat3n_dna.split_reads.R2.bam"
        done
 
+       # tar up the r1 and r2 stats files
+       tar -zcvf ../hisat3n_dna_split_reads_summary.R1.tar.gz *.hisat3n_dna_split_reads_summary.R1.txt
+       tar -zcvf ../hisat3n_dna_split_reads_summary.R2.tar.gz *.hisat3n_dna_split_reads_summary.R2.txt
+
+
        # define lists of r1 and r2 bam files
        R1_bams=($(ls | grep "\.hisat3n_dna.split_reads.R1.bam"))
        R2_bams=($(ls | grep "\.hisat3n_dna.split_reads.R2.bam"))
@@ -573,6 +578,8 @@ task Hisat_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name
     }
     output {
         File merge_sorted_bam_tar = "hisat3n_dna.split_reads.name_sort.bam.tar.gz"
+        File hisat3n_dna_split_reads_summary_R1_tar = "hisat3n_dna_split_reads_summary.R1.tar.gz"
+        File hisat3n_dna_split_reads_summary_R2_tar = "hisat3n_dna_split_reads_summary.R2.tar.gz"
     }
 }
 
@@ -748,7 +755,7 @@ task dedup_unique_bam_and_index_unique_bam {
           echo $name
           echo "Call Picard"
           picard MarkDuplicates I=$file O=/cromwell_root/output_bams/$name.bam \
-          M=/cromwell_root/output_bams/$name.matrix.stats \
+          M=/cromwell_root/output_bams/$name.matrix.txt \
           REMOVE_DUPLICATES=true TMP_DIR=/cromwell_root/temp
           echo "Call samtools index"
           samtools index /cromwell_root/output_bams/$name.bam
@@ -759,6 +766,9 @@ task dedup_unique_bam_and_index_unique_bam {
         #tar up the output files
         tar -zcvf dedup_unique_bam_and_index_unique_bam.tar.gz output_bams
 
+        #tar up the stats files
+        tar -zcvf dedup_unique_bam_and_index_unique_bam_stats.tar.gz output_bams/*.matrix.txt
+
     >>>
     runtime {
         docker: docker
@@ -768,6 +778,7 @@ task dedup_unique_bam_and_index_unique_bam {
     }
     output {
         File output_tar = "dedup_unique_bam_and_index_unique_bam.tar.gz"
+        File dedup_stats_tar = "dedup_unique_bam_and_index_unique_bam_stats.tar.gz"
     }
 }
 
@@ -893,26 +904,66 @@ task unique_reads_cgn_extraction {
 }
 
 
-#task summary {
-#    input {
-#        File trimmed_stats
-#        File hisat3n_stats
-#        File r1_hisat3n_stats
-#        File r2_hisat3n_stats
-#        File dedup_stats
-#        File chromatin_contact_stats
-#        File allc_uniq_reads_stats
-#        File unique_reads_cgn_extraction_tbi
-#    }
-#    command <<<
-#    >>>
-#    runtime {
-#        docker: "fill_in"
-#        disks: "local-disk ${disk_size} HDD"
-#        cpu: 1
-#        memory: "${mem_size} GiB"
-#    }
-#    output {
-#        File mapping_summary = "MappingSummary.csv.gz"
-#    }
-#}
+task summary {
+    input {
+        File trimmed_stats
+        File hisat3n_stats
+        File r1_hisat3n_stats
+        File r2_hisat3n_stats
+        File dedup_stats
+        File chromatin_contact_stats
+        File allc_uniq_reads_stats
+        File unique_reads_cgn_extraction_tbi
+        String docker = "us.gcr.io/broad-gotc-prod/m3c-yap-hisat:1.0.0-2.2.1"
+        Int disk_size = 80
+        Int mem_size = 20
+    }
+    command <<<
+        set -euo pipefail
+        mkdir /cromwell_root/fastq
+        mkdir /cromwell_root/bam
+        mkdir /cromwell_root/allc
+        mkdir /cromwell_root/hic
+
+        tar -xf ~{trimmed_stats}
+        rm ~{trimmed_stats}
+        tar -xf ~{hisat3n_stats}
+        rm ~{hisat3n_stats}
+        tar -xf ~{r1_hisat3n_stats}
+        rm ~{r1_hisat3n_stats}
+        tar -xf ~{r2_hisat3n_stats}
+        rm ~{r2_hisat3n_stats}
+        tar -xf ~{dedup_stats}
+        rm ~{dedup_stats}
+        tar -xf ~{chromatin_contact_stats}
+        rm ~{chromatin_contact_stats}
+        tar -xf ~{allc_uniq_reads_stats}
+        rm ~{allc_uniq_reads_stats}
+        tar -xf ~{unique_reads_cgn_extraction_tbi}
+        rm ~{unique_reads_cgn_extraction_tbi}
+
+        mv *.trimmed.stats.txt /cromwell_root/fastq
+        mv *.hisat3n_dna_summary.txt /cromwell_root/bam
+        mv *.hisat3n_dna_split_reads_summary.R1.txt /cromwell_root/bam
+        mv *.hisat3n_dna_split_reads_summary.R2.txt /cromwell_root/bam
+        mv output_bams/*.hisat3n_dna.all_reads.deduped.matrix.txt /cromwell_root/bam
+        mv *.hisat3n_dna.all_reads.contact_stats.csv /cromwell_root/hic
+        mv *.allc.tsv.gz.count.csv /cromwell_root/allc
+        mv cromwell_root/allc-CGN/*.allc.tsv.gz.tbi /cromwell_root/allc
+
+        python3 <<CODE
+        from cemba_data.hisat3n import *
+        snm3c_summary()
+        CODE
+
+       >>>
+    runtime {
+        docker: docker
+        disks: "local-disk ${disk_size} HDD"
+        cpu: 1
+        memory: "${mem_size} GiB"
+    }
+    output {
+        File mapping_summary = "MappingSummary.csv.gz"
+    }
+}

From d5037438b47e75a982ada01f01523bffe7842b4c Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Mon, 8 Jan 2024 14:19:25 -0500
Subject: [PATCH 02/23] add multimapper option

---
 pipelines/skylab/multiome/Multiome.wdl  |  2 ++
 pipelines/skylab/optimus/Optimus.wdl    |  4 +++-
 tasks/skylab/StarAlign.wdl              | 29 ++++++++++++++++---------
 verification/test-wdls/TestMultiome.wdl |  4 +++-
 4 files changed, 27 insertions(+), 12 deletions(-)

diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
index cc65819124..341a7ed60e 100644
--- a/pipelines/skylab/multiome/Multiome.wdl
+++ b/pipelines/skylab/multiome/Multiome.wdl
@@ -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
diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
index 98d10bbc52..eaa09a6dd8 100644
--- 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
@@ -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 {
diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl
index ce3600dc74..068efe78ab 100644
--- 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 +378,11 @@ task STARsoloFastq {
 
     if [[ "~{counting_mode}" == "sc_rna" ]]
     then
+      SoloDirectory="Solo.out/Gene/raw"
+      find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/
       mv "Solo.out/Gene/raw/barcodes.tsv" barcodes.tsv
       mv "Solo.out/Gene/raw/features.tsv" features.tsv
-      mv "Solo.out/Gene/raw/matrix.mtx"   matrix.mtx
+      #mv "Solo.out/Gene/raw/matrix.mtx"   Ithinkicandeletehismatrix.mtx
       mv "Solo.out/Gene/CellReads.stats" CellReads.stats
       mv "Solo.out/Gene/Features.stats" Features.stats
       mv "Solo.out/Gene/Summary.csv" Summary.csv
@@ -388,24 +391,30 @@ task STARsoloFastq {
     then
       if [[ "~{count_exons}" == "false" ]]
       then
+        SoloDirectory="Solo.out/GeneFull_Ex50pAS/raw"
+        find "$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/raw/matrix.mtx"   Ithinkicandeletehismatrix.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"
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/
+        SoloDirectory="Solo.out/Gene/raw"
+        find "$directory" -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/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
diff --git a/verification/test-wdls/TestMultiome.wdl b/verification/test-wdls/TestMultiome.wdl
index 9f35f7b8ae..1598f66714 100644
--- 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
   
     }
 

From 693c9326687b9b930e02a2a02300c416dd109072 Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Mon, 8 Jan 2024 15:43:51 -0500
Subject: [PATCH 03/23] update optimus plumbing for ease of testing

---
 .../test_inputs/Plumbing/human_v3_example.json       | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json b/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json
index ff5a02caaf..0e5fafca34 100644
--- a/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json
+++ b/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json
@@ -1,20 +1,18 @@
 {
   "Optimus.r1_fastq": [
-      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L001_R1_001.filtered.fastq.gz",
-      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L002_R1_001.filtered.fastq.gz"
+      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L001_R1_001.filtered.fastq.gz"
   ],
   "Optimus.r2_fastq": [
-      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L001_R2_001.filtered.fastq.gz",
-      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L002_R2_001.filtered.fastq.gz"
+      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L001_R2_001.filtered.fastq.gz"
   ],
   "Optimus.i1_fastq": [
-      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L001_I1_001.filtered.fastq.gz",
-      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L002_I1_001.filtered.fastq.gz"
+      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L001_I1_001.filtered.fastq.gz"
   ],
   "Optimus.tar_star_reference": "gs://gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_star2.7.10a-Human-GENCODE-build-GRCh38-43.tar",
   "Optimus.input_id": "pbmc_human_v3",
   "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"
 }

From 50b75ac21e9d89a02c3a3d3f96bdb518f5d0824a Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Mon, 8 Jan 2024 15:47:25 -0500
Subject: [PATCH 04/23] add echos

---
 .../Plumbing/mouse_v2_snRNA_example.json       | 18 ++----------------
 tasks/skylab/StarAlign.wdl                     | 12 ++++++++----
 2 files changed, 10 insertions(+), 20 deletions(-)

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
index 239b7d1fcb..f3cf14c382 100644
--- a/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_snRNA_example.json
+++ b/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_snRNA_example.json
@@ -1,23 +1,9 @@
 {
   "Optimus.r1_fastq": [
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L001_R1_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L002_R1_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L003_R1_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L004_R1_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L005_R1_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L006_R1_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L007_R1_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L008_R1_001.fastq.gz"
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L001_R1_001.fastq.gz"
   ],
   "Optimus.r2_fastq": [
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L001_R2_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L002_R2_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L003_R2_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L004_R2_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L005_R2_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L006_R2_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L007_R2_001.fastq.gz",
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L008_R2_001.fastq.gz"
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L001_R2_001.fastq.gz"
   ],
   "Optimus.tar_star_reference": "gs://gcp-public-data--broad-references/GRCm39/star/v2_7_10a/modified_star2.7.10a-Mouse-GENCODE-build-GRCm39-M32.tar",
   "Optimus.input_id": "nuclei_2k_mouse",
diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl
index 068efe78ab..3b6919948e 100644
--- a/tasks/skylab/StarAlign.wdl
+++ b/tasks/skylab/StarAlign.wdl
@@ -379,7 +379,8 @@ task STARsoloFastq {
     if [[ "~{counting_mode}" == "sc_rna" ]]
     then
       SoloDirectory="Solo.out/Gene/raw"
-      find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/
+      find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} mv {} /cromwell_root/
+      find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} mv {} /cromwell_root/
       mv "Solo.out/Gene/raw/barcodes.tsv" barcodes.tsv
       mv "Solo.out/Gene/raw/features.tsv" features.tsv
       #mv "Solo.out/Gene/raw/matrix.mtx"   Ithinkicandeletehismatrix.mtx
@@ -392,7 +393,8 @@ task STARsoloFastq {
       if [[ "~{count_exons}" == "false" ]]
       then
         SoloDirectory="Solo.out/GeneFull_Ex50pAS/raw"
-        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} mv {} /cromwell_root/
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo 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"   Ithinkicandeletehismatrix.mtx
@@ -402,9 +404,11 @@ task STARsoloFastq {
         mv "Solo.out/GeneFull_Ex50pAS/UMIperCellSorted.txt" UMIperCellSorted.txt
       else
         SoloDirectory="Solo.out/GeneFull_Ex50pAS/raw"
-        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} mv {} /cromwell_root/
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} mv {} /cromwell_root/
         SoloDirectory="Solo.out/Gene/raw"
-        find "$directory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} sh -c 'new_name="$(basename {} .mtx)_sn_rna.mtx"; mv {} "/cromwell_root/$new_name"'
+        find "$directory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} sh -c 'new_name="$(basename {} .mtx)_sn_rna.mtx"; mv {} "/cromwell_root/$new_name"'
+        find "$directory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo 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

From 10b42486514345078ab9d83b5051f99acc6d6a9b Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Mon, 8 Jan 2024 15:48:23 -0500
Subject: [PATCH 05/23] add to test

---
 verification/test-wdls/TestOptimus.wdl | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/verification/test-wdls/TestOptimus.wdl b/verification/test-wdls/TestOptimus.wdl
index b162ab1e35..535eb8d530 100644
--- 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

From b52cbf18395b5cb290d07122c499862967122497 Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Tue, 9 Jan 2024 08:54:00 -0500
Subject: [PATCH 06/23] remove some echoes

---
 tasks/skylab/StarAlign.wdl | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl
index 3b6919948e..100d856c81 100644
--- a/tasks/skylab/StarAlign.wdl
+++ b/tasks/skylab/StarAlign.wdl
@@ -379,8 +379,9 @@ 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 | echo xargs -0 -I{} mv {} /cromwell_root/
-      find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} mv {} /cromwell_root/
+      find "$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"   Ithinkicandeletehismatrix.mtx
@@ -393,8 +394,9 @@ task STARsoloFastq {
       if [[ "~{count_exons}" == "false" ]]
       then
         SoloDirectory="Solo.out/GeneFull_Ex50pAS/raw"
+        echo "SoloDirectory is $SoloDirectory"
         find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} mv {} /cromwell_root/
-        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} mv {} /cromwell_root/
+        find "$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"   Ithinkicandeletehismatrix.mtx
@@ -404,11 +406,13 @@ task STARsoloFastq {
         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 | echo xargs -0 -I{} mv {} /cromwell_root/
-        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} mv {} /cromwell_root/
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/
         SoloDirectory="Solo.out/Gene/raw"
+        echo "SoloDirectory is $SoloDirectory"
         find "$directory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} sh -c 'new_name="$(basename {} .mtx)_sn_rna.mtx"; mv {} "/cromwell_root/$new_name"'
-        find "$directory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} sh -c 'new_name="$(basename {} .mtx)_sn_rna.mtx"; mv {} "/cromwell_root/$new_name"'
+        find "$directory" -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

From 1949d4e675e8eb2e4e7ecdb9eb9727161c9a48d0 Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Tue, 9 Jan 2024 13:42:20 -0500
Subject: [PATCH 07/23] make mouse snrna json go back to what is in dev

---
 .../Plumbing/mouse_v2_snRNA_example.json       | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

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
index f3cf14c382..239b7d1fcb 100644
--- a/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_snRNA_example.json
+++ b/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_snRNA_example.json
@@ -1,9 +1,23 @@
 {
   "Optimus.r1_fastq": [
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L001_R1_001.fastq.gz"
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L001_R1_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L002_R1_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L003_R1_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L004_R1_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L005_R1_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L006_R1_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L007_R1_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L008_R1_001.fastq.gz"
   ],
   "Optimus.r2_fastq": [
-    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L001_R2_001.fastq.gz"
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L001_R2_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L002_R2_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L003_R2_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L004_R2_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L005_R2_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L006_R2_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L007_R2_001.fastq.gz",
+    "gs://broad-gotc-test-storage/Optimus/input/plumbing/mouse_v2/nuclei_2k_S1_L008_R2_001.fastq.gz"
   ],
   "Optimus.tar_star_reference": "gs://gcp-public-data--broad-references/GRCm39/star/v2_7_10a/modified_star2.7.10a-Mouse-GENCODE-build-GRCm39-M32.tar",
   "Optimus.input_id": "nuclei_2k_mouse",

From a330405def28885d9f271b98ef064bc110f8e633 Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Tue, 9 Jan 2024 13:44:10 -0500
Subject: [PATCH 08/23] make mouse snrna json go back to what is in dev

---
 .../optimus/test_inputs/Plumbing/human_v3_example.json   | 9 ++++++---
 .../optimus/test_inputs/Plumbing/mouse_v2_example.json   | 3 ++-
 .../test_inputs/Plumbing/mouse_v2_snRNA_example.json     | 3 ++-
 3 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json b/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json
index 0e5fafca34..240ae49ceb 100644
--- a/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json
+++ b/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json
@@ -1,12 +1,15 @@
 {
   "Optimus.r1_fastq": [
-      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L001_R1_001.filtered.fastq.gz"
+      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L001_R1_001.filtered.fastq.gz",
+      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L002_R1_001.filtered.fastq.gz"
   ],
   "Optimus.r2_fastq": [
-      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L001_R2_001.filtered.fastq.gz"
+      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L001_R2_001.filtered.fastq.gz",
+      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L002_R2_001.filtered.fastq.gz"
   ],
   "Optimus.i1_fastq": [
-      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L001_I1_001.filtered.fastq.gz"
+      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L001_I1_001.filtered.fastq.gz",
+      "gs://broad-gotc-test-storage/Optimus/input/plumbing/chemistry_10X_V3/pbmc_10k_v3_chr21_genic/pbmc_10k_v3_S1_L002_I1_001.filtered.fastq.gz"
   ],
   "Optimus.tar_star_reference": "gs://gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_star2.7.10a-Human-GENCODE-build-GRCh38-43.tar",
   "Optimus.input_id": "pbmc_human_v3",
diff --git a/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_example.json b/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_example.json
index bbf625ef27..60aa9d4cc6 100644
--- 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
index 239b7d1fcb..0afea7854b 100644
--- 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"
 }

From e4d2fa2dc340184681d4118acd4cd9da4448e872 Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Tue, 9 Jan 2024 14:08:23 -0500
Subject: [PATCH 09/23] add as outputs

---
 pipelines/skylab/multiome/Multiome.wdl |  5 +++++
 pipelines/skylab/optimus/Optimus.wdl   |  6 ++++++
 tasks/skylab/StarAlign.wdl             | 15 ++++++++-------
 3 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
index 341a7ed60e..e2d64133b4 100644
--- a/pipelines/skylab/multiome/Multiome.wdl
+++ b/pipelines/skylab/multiome/Multiome.wdl
@@ -136,6 +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/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
index eaa09a6dd8..e1dc99c2fc 100644
--- a/pipelines/skylab/optimus/Optimus.wdl
+++ b/pipelines/skylab/optimus/Optimus.wdl
@@ -239,6 +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/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl
index 100d856c81..2cedd9ac6d 100644
--- a/tasks/skylab/StarAlign.wdl
+++ b/tasks/skylab/StarAlign.wdl
@@ -380,11 +380,10 @@ task STARsoloFastq {
     then
       SoloDirectory="Solo.out/Gene/raw"
       echo "SoloDirectory is $SoloDirectory"
-      find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} mv {} /cromwell_root/
+      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"   Ithinkicandeletehismatrix.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
@@ -395,11 +394,10 @@ task STARsoloFastq {
       then
         SoloDirectory="Solo.out/GeneFull_Ex50pAS/raw"
         echo "SoloDirectory is $SoloDirectory"
-        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} mv {} /cromwell_root/
+        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"   Ithinkicandeletehismatrix.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
@@ -407,15 +405,14 @@ task STARsoloFastq {
       else
         SoloDirectory="Solo.out/GeneFull_Ex50pAS/raw"
         echo "SoloDirectory is $SoloDirectory"
-        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} mv {} /cromwell_root/
+        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 $SoloDirectory"
-        find "$directory" -maxdepth 1 -type f -name "*.mtx" -print0 | echo xargs -0 -I{} sh -c 'new_name="$(basename {} .mtx)_sn_rna.mtx"; mv {} "/cromwell_root/$new_name"'
+        find "$directory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} sh -c 'new_name="$(basename {} .mtx)_sn_rna.mtx";  echo mv {} "/cromwell_root/$new_name"'
         find "$directory" -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
@@ -462,6 +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"
   }
 }
 

From e75a479085637712173a99ed8f8dcd898ce8fd6e Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Wed, 10 Jan 2024 13:22:22 -0500
Subject: [PATCH 10/23] typo

---
 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 2cedd9ac6d..5dead400a5 100644
--- a/tasks/skylab/StarAlign.wdl
+++ b/tasks/skylab/StarAlign.wdl
@@ -409,8 +409,8 @@ task STARsoloFastq {
         find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/
         SoloDirectory="Solo.out/Gene/raw"
         echo "SoloDirectory is $SoloDirectory"
-        find "$directory" -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 "$directory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} sh -c 'new_name="$(basename {} .mtx)_sn_rna.mtx"; mv {} "/cromwell_root/$new_name"'
+        find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} sh -c 'new_name="$(basename {} .mtx)_sn_rna.mtx";  echo mv {} "/cromwell_root/$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/CellReads.stats" CellReads.stats

From bab93adb9f755436a8a42a0df165f5417e6da9d0 Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Thu, 11 Jan 2024 09:03:44 -0500
Subject: [PATCH 11/23] changelogs

---
 pipelines/skylab/multiome/Multiome.changelog.md              | 5 +++++
 pipelines/skylab/multiome/Multiome.wdl                       | 2 +-
 pipelines/skylab/optimus/Optimus.changelog.md                | 4 ++++
 pipelines/skylab/optimus/Optimus.wdl                         | 2 +-
 pipelines/skylab/paired_tag/PairedTag.changelog.md           | 4 ++++
 pipelines/skylab/paired_tag/PairedTag.wdl                    | 2 +-
 pipelines/skylab/slideseq/SlideSeq.changelog.md              | 4 ++++
 pipelines/skylab/slideseq/SlideSeq.wdl                       | 2 +-
 .../MultiSampleSmartSeq2SingleNucleus.changelog.md           | 4 ++++
 .../MultiSampleSmartSeq2SingleNucleus.wdl                    | 2 +-
 10 files changed, 26 insertions(+), 5 deletions(-)

diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
index 48070c0ec9..457c6cd2de 100644
--- 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
index e2d64133b4..4967be0351 100644
--- 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
diff --git a/pipelines/skylab/optimus/Optimus.changelog.md b/pipelines/skylab/optimus/Optimus.changelog.md
index 489343f6c1..2c0e1cb730 100644
--- 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
index e1dc99c2fc..146be378ee 100644
--- a/pipelines/skylab/optimus/Optimus.wdl
+++ b/pipelines/skylab/optimus/Optimus.wdl
@@ -65,7 +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))
diff --git a/pipelines/skylab/paired_tag/PairedTag.changelog.md b/pipelines/skylab/paired_tag/PairedTag.changelog.md
index eb236702ce..a7a173d46f 100644
--- 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
index 36816f514d..59d24db8d8 100644
--- 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
index 3b3f2cec69..969c9782cc 100644
--- 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
index fcd7238683..e088379862 100644
--- 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/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
index f64b820dd3..6ab189b9ce 100644
--- a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
+++ b/pipelines/skylab/smartseq2_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
index 23fa349662..d0bf9dbb2f 100644
--- 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"

From 3aeca876694a4c1c8b8291d2345d3950b53fd57c Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Thu, 11 Jan 2024 10:46:02 -0500
Subject: [PATCH 12/23] changelogs

---
 .../multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pipelines/skylab/multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json b/pipelines/skylab/multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json
index c394ae790c..352e345c47 100644
--- 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.Optimus.STARsoloFastq.soloMultiMappers":"Uniform"
 }

From e8fde9f00bac07a86d2867fc2ed6b0379a59d46c Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Thu, 11 Jan 2024 11:42:57 -0500
Subject: [PATCH 13/23] changelogs

---
 .../multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipelines/skylab/multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json b/pipelines/skylab/multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json
index 352e345c47..3c3b223256 100644
--- a/pipelines/skylab/multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json
+++ b/pipelines/skylab/multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json
@@ -24,5 +24,5 @@
   "Multiome.Atac.BWAPairedEndAlignment.cpu_platform":"Intel Cascade Lake",
   "Multiome.Atac.BWAPairedEndAlignment.mem_size":"64",
   "Multiome.Atac.BWAPairedEndAlignment.nthreads":"16",
-  "Multiome.Optimus.STARsoloFastq.soloMultiMappers":"Uniform"
+  "Multiome.soloMultiMappers":"Uniform"
 }

From 660c1ec372fee282e5ab6b536091baf947c4f2ef Mon Sep 17 00:00:00 2001
From: kayleemathews <kmathews@broadinstitute.org>
Date: Fri, 12 Jan 2024 09:28:57 -0500
Subject: [PATCH 14/23] update pipeline docs

---
 website/docs/Pipelines/Multiome_Pipeline/README.md        | 8 +++++++-
 website/docs/Pipelines/Optimus_Pipeline/README.md         | 8 +++++++-
 website/docs/Pipelines/PairedTag_Pipeline/README.md       | 2 +-
 .../README.md                                             | 2 +-
 4 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md
index 413e6addcf..757457170f 100644
--- 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. |
diff --git a/website/docs/Pipelines/Optimus_Pipeline/README.md b/website/docs/Pipelines/Optimus_Pipeline/README.md
index d59477bf45..2032919528 100644
--- a/website/docs/Pipelines/Optimus_Pipeline/README.md
+++ b/website/docs/Pipelines/Optimus_Pipeline/README.md
@@ -7,7 +7,7 @@ slug: /Pipelines/Optimus_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [optimus_v6.3.2](https://github.com/broadinstitute/warp/releases?q=optimus&expanded=true) | December, 2023 | Elizabeth Kiernan | Please file GitHub issues in warp or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) |
+| [optimus_v6.3.4](https://github.com/broadinstitute/warp/releases?q=optimus&expanded=true) | January, 2024 | Elizabeth Kiernan | Please file GitHub issues in warp or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) |
 
 ![Optimus_diagram](Optimus_diagram.png)
 
@@ -93,6 +93,7 @@ The example configuration files also contain metadata for the reference files, d
 | annotations_gtf | GTF containing gene annotations used for gene tagging (must match GTF in STAR reference). | N/A |
 | tenx_chemistry_version | Integer that specifies if data was generated with 10x v2 or v3 chemistry. Optimus validates this chemistry by examining the UMIs and CBs in the first read 1 FASTQ file. If the chemistry does not match, the pipeline will fail. You can remove the check by setting "ignore_r1_read_length = true" in the input JSON. | 2 or 3 |
 | mt_genes | Optional file containing mitochondrial gene names for a specific species. This is used for calculating gene metrics. | N/A |
+| soloMultiMappers | Optional string describing whether or not the Optimus (GEX) pipeline should run STARsolo with the `--soloMultiMappers` flag. | N/A |
 | counting_mode | String describing whether data is single-cell or single-nucleus. Single-cell mode counts reads aligned to the gene transcript, whereas single-nucleus counts whole transcript to account for nuclear pre-mRNA. | "sc_rna" or "sn_rna" |
 | output_bam_basename | String used as a basename for output BAM file; the default is set to the string used for the `input_id` parameter. | N/A |
 | star_strand_mode | Optional string for running the workflow on forward stranded, reverse stranded, or unstranded data; default is "Forward". | "Forward" (default), "Reverse", and "Unstranded" |
@@ -252,6 +253,11 @@ The following table lists the output files produced from the pipeline. For sampl
 | cell_metrics | `<input_id>.cell-metrics.csv.gz` | Matrix of metrics by cells. | Compressed CSV |
 | gene_metrics | `<input_id>.gene-metrics.csv.gz` |  Matrix of metrics by genes. | Compressed CSV |
 | aligner_metrics | `<input_id>.cell_reads.txt` | Per barcode metrics (CellReads.stats) produced by the STARsolo aligner. | TXT |
+| soloMultiMappers |
+| multimappers_EM_matrix |
+| multimappers_Uniform_matrix |
+| multimappers_Rescue_matrix |
+| multimappers_PropUnique_matrix |
 | cell_calls | empty_drops_result.csv | emptyDrops results from the RunEmptyDrops task. | CSV |
 | h5ad_output_file | `<input_id>.h5ad` | h5ad file with count data (exonic or whole transcript depending on the counting_mode) and metadata. | H5AD |
 
diff --git a/website/docs/Pipelines/PairedTag_Pipeline/README.md b/website/docs/Pipelines/PairedTag_Pipeline/README.md
index 5b7e7b0a02..86ddd12d87 100644
--- a/website/docs/Pipelines/PairedTag_Pipeline/README.md
+++ b/website/docs/Pipelines/PairedTag_Pipeline/README.md
@@ -7,7 +7,7 @@ slug: /Pipelines/PairedTag_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [PairedTag_v0.0.3](https://github.com/broadinstitute/warp/releases) | January, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact [documentation authors](mailto:warp-pipelines-help@broadinstitute.org) |
+| [PairedTag_v0.0.4](https://github.com/broadinstitute/warp/releases) | January, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact [documentation authors](mailto:warp-pipelines-help@broadinstitute.org) |
 
 ## Introduction to the Paired-Tag workflow
 
diff --git a/website/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md b/website/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md
index bbfffebe12..e21fe808ee 100644
--- a/website/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md
+++ b/website/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md
@@ -7,7 +7,7 @@ slug: /Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [MultiSampleSmartSeq2SingleNuclei_v1.2.26](https://github.com/broadinstitute/warp/releases) | December, 2023 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in WARP or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) |
+| [MultiSampleSmartSeq2SingleNuclei_v1.2.28](https://github.com/broadinstitute/warp/releases) | January, 2024 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in WARP or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) |
 
 ![](./snSS2.png)
 

From fc80cdbf262bfd4e1dd44f7673004ec8bbcad5b9 Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Fri, 12 Jan 2024 13:32:30 -0500
Subject: [PATCH 15/23] optional output

---
 pipelines/skylab/multiome/Multiome.wdl | 2 +-
 pipelines/skylab/optimus/Optimus.wdl   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
index 4967be0351..8e91900157 100644
--- a/pipelines/skylab/multiome/Multiome.wdl
+++ b/pipelines/skylab/multiome/Multiome.wdl
@@ -136,7 +136,7 @@ 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?] 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
diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
index 146be378ee..45c2c6a5d7 100644
--- a/pipelines/skylab/optimus/Optimus.wdl
+++ b/pipelines/skylab/optimus/Optimus.wdl
@@ -239,7 +239,7 @@ 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?] 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

From 500ff512dfda2782366d229ab4eb4ccef356045d Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Fri, 12 Jan 2024 13:36:07 -0500
Subject: [PATCH 16/23] optional output

---
 pipelines/skylab/multiome/Multiome.wdl | 2 +-
 pipelines/skylab/optimus/Optimus.wdl   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
index 8e91900157..4967be0351 100644
--- a/pipelines/skylab/multiome/Multiome.wdl
+++ b/pipelines/skylab/multiome/Multiome.wdl
@@ -136,7 +136,7 @@ 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] 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
diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
index 45c2c6a5d7..146be378ee 100644
--- a/pipelines/skylab/optimus/Optimus.wdl
+++ b/pipelines/skylab/optimus/Optimus.wdl
@@ -239,7 +239,7 @@ 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] 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

From e8d911151b065184e8dfa40f8c03db93e68acfe6 Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Fri, 12 Jan 2024 13:49:49 -0500
Subject: [PATCH 17/23] optional output

---
 pipelines/skylab/multiome/Multiome.wdl             |  2 +-
 pipelines/skylab/optimus/Optimus.wdl               |  2 +-
 tasks/skylab/StarAlign.wdl                         |  1 -
 website/docs/Pipelines/Multiome_Pipeline/README.md | 10 +++++-----
 website/docs/Pipelines/Optimus_Pipeline/README.md  |  8 ++++----
 5 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
index 4967be0351..5634f9bf03 100644
--- a/pipelines/skylab/multiome/Multiome.wdl
+++ b/pipelines/skylab/multiome/Multiome.wdl
@@ -136,7 +136,7 @@ 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] matrix_sn_rna = 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
diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
index 146be378ee..7c6b01034c 100644
--- a/pipelines/skylab/optimus/Optimus.wdl
+++ b/pipelines/skylab/optimus/Optimus.wdl
@@ -239,7 +239,7 @@ 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] matrix_sn_rna = 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
diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl
index e9688bbdf7..8ab0c8d615 100644
--- a/tasks/skylab/StarAlign.wdl
+++ b/tasks/skylab/StarAlign.wdl
@@ -419,7 +419,6 @@ task STARsoloFastq {
         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/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
diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md
index 757457170f..2f5fb9fab7 100644
--- a/website/docs/Pipelines/Multiome_Pipeline/README.md
+++ b/website/docs/Pipelines/Multiome_Pipeline/README.md
@@ -115,11 +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 |
+| soloMultiMappers | 
+| multimappers_EM_matrix | UniqueAndMult-EM.mtx |
+| multimappers_Uniform_matrix | UniqueAndMult-Uniform.mtx |
+| multimappers_Rescue_matrix | UniqueAndMult-Rescue.mtx |
+| multimappers_PropUnique_matrix | UniqueAndMult-PropUnique.mtx |
 | 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. |
diff --git a/website/docs/Pipelines/Optimus_Pipeline/README.md b/website/docs/Pipelines/Optimus_Pipeline/README.md
index 2032919528..bb8fa67ebb 100644
--- a/website/docs/Pipelines/Optimus_Pipeline/README.md
+++ b/website/docs/Pipelines/Optimus_Pipeline/README.md
@@ -254,10 +254,10 @@ The following table lists the output files produced from the pipeline. For sampl
 | gene_metrics | `<input_id>.gene-metrics.csv.gz` |  Matrix of metrics by genes. | Compressed CSV |
 | aligner_metrics | `<input_id>.cell_reads.txt` | Per barcode metrics (CellReads.stats) produced by the STARsolo aligner. | TXT |
 | soloMultiMappers |
-| multimappers_EM_matrix |
-| multimappers_Uniform_matrix |
-| multimappers_Rescue_matrix |
-| multimappers_PropUnique_matrix |
+| multimappers_EM_matrix | UniqueAndMult-EM.mtx |
+| multimappers_Uniform_matrix | UniqueAndMult-Uniform.mtx |
+| multimappers_Rescue_matrix | UniqueAndMult-Rescue.mtx |
+| multimappers_PropUnique_matrix | UniqueAndMult-PropUnique.mtx |
 | cell_calls | empty_drops_result.csv | emptyDrops results from the RunEmptyDrops task. | CSV |
 | h5ad_output_file | `<input_id>.h5ad` | h5ad file with count data (exonic or whole transcript depending on the counting_mode) and metadata. | H5AD |
 

From 875fa4a9f27d82a0f428733ab0e2764ae6ea6f99 Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Fri, 12 Jan 2024 13:51:14 -0500
Subject: [PATCH 18/23] optional output

---
 pipelines/skylab/multiome/Multiome.wdl             | 1 -
 pipelines/skylab/optimus/Optimus.wdl               | 1 -
 website/docs/Pipelines/Multiome_Pipeline/README.md | 1 -
 website/docs/Pipelines/Optimus_Pipeline/README.md  | 1 -
 4 files changed, 4 deletions(-)

diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
index 5634f9bf03..e8c92430d5 100644
--- a/pipelines/skylab/multiome/Multiome.wdl
+++ b/pipelines/skylab/multiome/Multiome.wdl
@@ -136,7 +136,6 @@ 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] matrix_sn_rna = 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
diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
index 7c6b01034c..fb01379032 100644
--- a/pipelines/skylab/optimus/Optimus.wdl
+++ b/pipelines/skylab/optimus/Optimus.wdl
@@ -239,7 +239,6 @@ workflow Optimus {
     File gene_metrics = GeneMetrics.gene_metrics
     File? cell_calls = RunEmptyDrops.empty_drops_result
     File? aligner_metrics = MergeStarOutputs.cell_reads_out
-    Array[File] matrix_sn_rna = 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
diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md
index 2f5fb9fab7..c99d5e89d5 100644
--- a/website/docs/Pipelines/Multiome_Pipeline/README.md
+++ b/website/docs/Pipelines/Multiome_Pipeline/README.md
@@ -115,7 +115,6 @@ 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 | UniqueAndMult-EM.mtx |
 | multimappers_Uniform_matrix | UniqueAndMult-Uniform.mtx |
 | multimappers_Rescue_matrix | UniqueAndMult-Rescue.mtx |
diff --git a/website/docs/Pipelines/Optimus_Pipeline/README.md b/website/docs/Pipelines/Optimus_Pipeline/README.md
index bb8fa67ebb..70b50069fc 100644
--- a/website/docs/Pipelines/Optimus_Pipeline/README.md
+++ b/website/docs/Pipelines/Optimus_Pipeline/README.md
@@ -253,7 +253,6 @@ The following table lists the output files produced from the pipeline. For sampl
 | cell_metrics | `<input_id>.cell-metrics.csv.gz` | Matrix of metrics by cells. | Compressed CSV |
 | gene_metrics | `<input_id>.gene-metrics.csv.gz` |  Matrix of metrics by genes. | Compressed CSV |
 | aligner_metrics | `<input_id>.cell_reads.txt` | Per barcode metrics (CellReads.stats) produced by the STARsolo aligner. | TXT |
-| soloMultiMappers |
 | multimappers_EM_matrix | UniqueAndMult-EM.mtx |
 | multimappers_Uniform_matrix | UniqueAndMult-Uniform.mtx |
 | multimappers_Rescue_matrix | UniqueAndMult-Rescue.mtx |

From 5ce21a44ce290aa89d7794a2c389f15838db9057 Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Fri, 12 Jan 2024 14:01:23 -0500
Subject: [PATCH 19/23] docs

---
 .../Pipelines/Multiome_Pipeline/README.md     | 22 +++++++++----------
 .../docs/Pipelines/Optimus_Pipeline/README.md |  8 +++----
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md
index c99d5e89d5..ea05e7238b 100644
--- a/website/docs/Pipelines/Multiome_Pipeline/README.md
+++ b/website/docs/Pipelines/Multiome_Pipeline/README.md
@@ -115,18 +115,18 @@ 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. |
-| multimappers_EM_matrix | UniqueAndMult-EM.mtx |
-| multimappers_Uniform_matrix | UniqueAndMult-Uniform.mtx |
-| multimappers_Rescue_matrix | UniqueAndMult-Rescue.mtx |
-| multimappers_PropUnique_matrix | UniqueAndMult-PropUnique.mtx |
-| 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. |
+| multimappers_EM_matrix | UniqueAndMult-EM.mtx | Optional output produced when `soloMultiMappers` is "EM"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.|
+| multimappers_Uniform_matrix | UniqueAndMult-Uniform.mtx | Optional output produced when `soloMultiMappers` is "Uniform"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.|
+| multimappers_Rescue_matrix | UniqueAndMult-Rescue.mtx | Optional output produced when `soloMultiMappers` is "Rescue"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information. |
+| multimappers_PropUnique_matrix | UniqueAndMult-PropUnique.mtx | Optional output produced when `soloMultiMappers` is "PropUnique"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.|
+| 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. |
-| html_report_array | `<report_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. |
-| log | `<log>` | 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. |
-| metrics_csv_array | `<metrics_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. |
-| output_directory | `<output_dir>` | 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. |
-| summary_pdf | `<pdf>` | 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.|
+| html_report_array | `<report_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.|
+| log | `<log>` | 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.|
+| metrics_csv_array | `<metrics_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.|
+| output_directory | `<output_dir>` | 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.|
+| summary_pdf | `<pdf>` | 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.|
 
 
 
diff --git a/website/docs/Pipelines/Optimus_Pipeline/README.md b/website/docs/Pipelines/Optimus_Pipeline/README.md
index 70b50069fc..8df2979d25 100644
--- a/website/docs/Pipelines/Optimus_Pipeline/README.md
+++ b/website/docs/Pipelines/Optimus_Pipeline/README.md
@@ -253,10 +253,10 @@ The following table lists the output files produced from the pipeline. For sampl
 | cell_metrics | `<input_id>.cell-metrics.csv.gz` | Matrix of metrics by cells. | Compressed CSV |
 | gene_metrics | `<input_id>.gene-metrics.csv.gz` |  Matrix of metrics by genes. | Compressed CSV |
 | aligner_metrics | `<input_id>.cell_reads.txt` | Per barcode metrics (CellReads.stats) produced by the STARsolo aligner. | TXT |
-| multimappers_EM_matrix | UniqueAndMult-EM.mtx |
-| multimappers_Uniform_matrix | UniqueAndMult-Uniform.mtx |
-| multimappers_Rescue_matrix | UniqueAndMult-Rescue.mtx |
-| multimappers_PropUnique_matrix | UniqueAndMult-PropUnique.mtx |
+| multimappers_EM_matrix | UniqueAndMult-EM.mtx | Optional output produced when `soloMultiMappers` is "EM"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information. | MTX |
+| multimappers_Uniform_matrix | UniqueAndMult-Uniform.mtx | Optional output produced when `soloMultiMappers` is "Uniform"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information. | MTX |
+| multimappers_Rescue_matrix | UniqueAndMult-Rescue.mtx | Optional output produced when `soloMultiMappers` is "Rescue"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information. | MTX |
+| multimappers_PropUnique_matrix | UniqueAndMult-PropUnique.mtx | Optional output produced when `soloMultiMappers` is "PropUnique"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.| MTX |
 | cell_calls | empty_drops_result.csv | emptyDrops results from the RunEmptyDrops task. | CSV |
 | h5ad_output_file | `<input_id>.h5ad` | h5ad file with count data (exonic or whole transcript depending on the counting_mode) and metadata. | H5AD |
 

From a8223df0889c4e37f6d9ff8947f0af7ce57c485c Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Fri, 12 Jan 2024 14:07:44 -0500
Subject: [PATCH 20/23] docs

---
 website/docs/Pipelines/Multiome_Pipeline/README.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md
index ea05e7238b..a1ae09b092 100644
--- a/website/docs/Pipelines/Multiome_Pipeline/README.md
+++ b/website/docs/Pipelines/Multiome_Pipeline/README.md
@@ -121,12 +121,12 @@ The Multiome workflow calls two WARP subworkflows, one external subworkflow (opt
 | multimappers_PropUnique_matrix | UniqueAndMult-PropUnique.mtx | Optional output produced when `soloMultiMappers` is "PropUnique"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.|
 | 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.|
-| html_report_array | `<report_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.|
-| log | `<log>` | 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.|
-| metrics_csv_array | `<metrics_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.|
-| output_directory | `<output_dir>` | 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.|
-| summary_pdf | `<pdf>` | 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. |
+| html_report_array | `<report_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. |
+| log | `<log>` | 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. |
+| metrics_csv_array | `<metrics_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. |
+| output_directory | `<output_dir>` | 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. |
+| summary_pdf | `<pdf>` | 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.n |
 
 
 

From 21e8d378313c1e76d9dacadc21400fe31365b7e2 Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Fri, 12 Jan 2024 14:08:52 -0500
Subject: [PATCH 21/23] docs

---
 website/docs/Pipelines/Multiome_Pipeline/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md
index a1ae09b092..3057f89507 100644
--- a/website/docs/Pipelines/Multiome_Pipeline/README.md
+++ b/website/docs/Pipelines/Multiome_Pipeline/README.md
@@ -126,7 +126,7 @@ The Multiome workflow calls two WARP subworkflows, one external subworkflow (opt
 | log | `<log>` | 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. |
 | metrics_csv_array | `<metrics_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. |
 | output_directory | `<output_dir>` | 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. |
-| summary_pdf | `<pdf>` | 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.n |
+| summary_pdf | `<pdf>` | 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. |
 
 
 

From 47a6197f1b17f463e7975c708993af3769da4ad6 Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <38223776+nikellepetrillo@users.noreply.github.com>
Date: Tue, 16 Jan 2024 09:13:50 -0500
Subject: [PATCH 22/23] Update
 website/docs/Pipelines/Optimus_Pipeline/README.md

Co-authored-by: Kaylee Mathews <95316074+kayleemathews@users.noreply.github.com>
---
 website/docs/Pipelines/Optimus_Pipeline/README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/website/docs/Pipelines/Optimus_Pipeline/README.md b/website/docs/Pipelines/Optimus_Pipeline/README.md
index 8df2979d25..71b18e89c5 100644
--- a/website/docs/Pipelines/Optimus_Pipeline/README.md
+++ b/website/docs/Pipelines/Optimus_Pipeline/README.md
@@ -253,10 +253,10 @@ The following table lists the output files produced from the pipeline. For sampl
 | cell_metrics | `<input_id>.cell-metrics.csv.gz` | Matrix of metrics by cells. | Compressed CSV |
 | gene_metrics | `<input_id>.gene-metrics.csv.gz` |  Matrix of metrics by genes. | Compressed CSV |
 | aligner_metrics | `<input_id>.cell_reads.txt` | Per barcode metrics (CellReads.stats) produced by the STARsolo aligner. | TXT |
-| multimappers_EM_matrix | UniqueAndMult-EM.mtx | Optional output produced when `soloMultiMappers` is "EM"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information. | MTX |
-| multimappers_Uniform_matrix | UniqueAndMult-Uniform.mtx | Optional output produced when `soloMultiMappers` is "Uniform"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information. | MTX |
-| multimappers_Rescue_matrix | UniqueAndMult-Rescue.mtx | Optional output produced when `soloMultiMappers` is "Rescue"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information. | MTX |
-| multimappers_PropUnique_matrix | UniqueAndMult-PropUnique.mtx | Optional output produced when `soloMultiMappers` is "PropUnique"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.| MTX |
+| multimappers_EM_matrix | `UniqueAndMult-EM.mtx` | Optional output produced when `soloMultiMappers` is "EM"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information. | MTX |
+| multimappers_Uniform_matrix | `UniqueAndMult-Uniform.mtx` | Optional output produced when `soloMultiMappers` is "Uniform"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information. | MTX |
+| multimappers_Rescue_matrix | `UniqueAndMult-Rescue.mtx` | Optional output produced when `soloMultiMappers` is "Rescue"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information. | MTX |
+| multimappers_PropUnique_matrix | `UniqueAndMult-PropUnique.mtx` | Optional output produced when `soloMultiMappers` is "PropUnique"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.| MTX |
 | cell_calls | empty_drops_result.csv | emptyDrops results from the RunEmptyDrops task. | CSV |
 | h5ad_output_file | `<input_id>.h5ad` | h5ad file with count data (exonic or whole transcript depending on the counting_mode) and metadata. | H5AD |
 

From e72f185aa54c3f92038489d250443699a7970fda Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <npetrill@broadinstitute.org>
Date: Tue, 16 Jan 2024 09:16:18 -0500
Subject: [PATCH 23/23] remove optional input to tests

---
 .../skylab/optimus/test_inputs/Plumbing/human_v3_example.json  | 3 +--
 .../skylab/optimus/test_inputs/Plumbing/mouse_v2_example.json  | 3 +--
 .../optimus/test_inputs/Plumbing/mouse_v2_snRNA_example.json   | 3 +--
 3 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json b/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json
index 240ae49ceb..ff5a02caaf 100644
--- a/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json
+++ b/pipelines/skylab/optimus/test_inputs/Plumbing/human_v3_example.json
@@ -16,6 +16,5 @@
   "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.soloMultiMappers": "EM"
+  "Optimus.ref_genome_fasta": "gs://gcp-public-data--broad-references/hg38/v0/GRCh38.primary_assembly.genome.fa"
 }
diff --git a/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_example.json b/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_example.json
index 60aa9d4cc6..bbf625ef27 100644
--- a/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_example.json
+++ b/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_example.json
@@ -28,6 +28,5 @@
   "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.soloMultiMappers": "EM"
+  "Optimus.ref_genome_fasta": "gs://gcp-public-data--broad-references/GRCm39/GRCm39.primary_assembly.genome.fa.gz"
 }
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
index 0afea7854b..239b7d1fcb 100644
--- a/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_snRNA_example.json
+++ b/pipelines/skylab/optimus/test_inputs/Plumbing/mouse_v2_snRNA_example.json
@@ -26,6 +26,5 @@
   "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.soloMultiMappers": "EM"
+  "Optimus.count_exons": true
 }