diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md index 836ec98fd8..c6746ea1aa 100644 --- a/pipelines/skylab/multiome/Multiome.changelog.md +++ b/pipelines/skylab/multiome/Multiome.changelog.md @@ -1,8 +1,9 @@ # 3.0.5 -2024-01-10 (Date of Last Commit) +2024-01-11 (Date of Last Commit) * Increased memory for MergeStarOutputs in StarAlign.wdl, RunEmptyDrops in RunEmptyDrops.wdl, OptimusH5ad in H5adUtils.wdl and GeneMetrics in Metrics.wdl - +* 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 1afd921e84..e8c92430d5 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 @@ -134,6 +136,10 @@ workflow Multiome { File gene_metrics_gex = Optimus.gene_metrics File? cell_calls_gex = Optimus.cell_calls File h5ad_output_file_gex = JoinBarcodes.gex_h5ad_file + Array[File?] multimappers_EM_matrix = Optimus.multimappers_EM_matrix + Array[File?] multimappers_Uniform_matrix = Optimus.multimappers_Uniform_matrix + Array[File?] multimappers_Rescue_matrix = Optimus.multimappers_Rescue_matrix + Array[File?] multimappers_PropUnique_matrix = Optimus.multimappers_PropUnique_matrix # cellbender outputs File? cell_barcodes_csv = CellBender.cell_csv diff --git a/pipelines/skylab/multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json b/pipelines/skylab/multiome/test_inputs/Plumbing/10k_pbmc_downsampled.json index c394ae790c..3c3b223256 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.soloMultiMappers":"Uniform" } diff --git a/pipelines/skylab/optimus/Optimus.changelog.md b/pipelines/skylab/optimus/Optimus.changelog.md index ee28052bf5..b545ab05ee 100644 --- a/pipelines/skylab/optimus/Optimus.changelog.md +++ b/pipelines/skylab/optimus/Optimus.changelog.md @@ -1,7 +1,8 @@ # 6.3.4 -2024-01-10 (Date of Last Commit) +2024-01-11 (Date of Last Commit) * Increased memory for MergeStarOutputs in StarAlign.wdl, RunEmptyDrops in RunEmptyDrops.wdl, OptimusH5ad in H5adUtils.wdl and GeneMetrics in Metrics.wdl - +* 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 aee7726f8d..fb01379032 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 { @@ -237,6 +239,11 @@ workflow Optimus { File gene_metrics = GeneMetrics.gene_metrics File? cell_calls = RunEmptyDrops.empty_drops_result File? aligner_metrics = MergeStarOutputs.cell_reads_out + Array[File?] multimappers_EM_matrix = STARsoloFastq.multimappers_EM_matrix + Array[File?] multimappers_Uniform_matrix = STARsoloFastq.multimappers_Uniform_matrix + Array[File?] multimappers_Rescue_matrix = STARsoloFastq.multimappers_Rescue_matrix + Array[File?] multimappers_PropUnique_matrix = STARsoloFastq.multimappers_PropUnique_matrix + # h5ad File h5ad_output_file = final_h5ad_output } diff --git a/pipelines/skylab/paired_tag/PairedTag.changelog.md b/pipelines/skylab/paired_tag/PairedTag.changelog.md index 1b8f8d7085..f59f955172 100644 --- a/pipelines/skylab/paired_tag/PairedTag.changelog.md +++ b/pipelines/skylab/paired_tag/PairedTag.changelog.md @@ -1,8 +1,9 @@ # 0.0.4 -2024-01-10 (Date of Last Commit) +2024-01-11 (Date of Last Commit) * Increased memory for MergeStarOutputs in StarAlign.wdl, RunEmptyDrops in RunEmptyDrops.wdl, OptimusH5ad in H5adUtils.wdl and GeneMetrics in Metrics.wdl - +* 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/slideseq/SlideSeq.changelog.md b/pipelines/skylab/slideseq/SlideSeq.changelog.md index da5cdf8059..2398c699e6 100644 --- a/pipelines/skylab/slideseq/SlideSeq.changelog.md +++ b/pipelines/skylab/slideseq/SlideSeq.changelog.md @@ -1,7 +1,8 @@ # 2.1.5 -2024-01-10 (Date of Last Commit) +2024-01-11 (Date of Last Commit) * Increased memory for MergeStarOutputs in StarAlign.wdl, RunEmptyDrops in RunEmptyDrops.wdl, OptimusH5ad in H5adUtils.wdl and GeneMetrics in Metrics.wdl +* 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) diff --git a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md index 50c2394d4b..b0e84df63f 100644 --- a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md +++ b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md @@ -1,8 +1,9 @@ # 1.2.28 -2024-01-10 (Date of Last Commit) +2024-01-11 (Date of Last Commit) * Increased memory for MergeStarOutputs in StarAlign.wdl, RunEmptyDrops in RunEmptyDrops.wdl, OptimusH5ad in H5adUtils.wdl and GeneMetrics in Metrics.wdl - +* 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) diff --git a/tasks/skylab/StarAlign.wdl b/tasks/skylab/StarAlign.wdl index d8cc5f243c..8ab0c8d615 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 +378,12 @@ task STARsoloFastq { if [[ "~{counting_mode}" == "sc_rna" ]] then + SoloDirectory="Solo.out/Gene/raw" + echo "SoloDirectory is $SoloDirectory" + find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} echo mv {} /cromwell_root/ + find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/ mv "Solo.out/Gene/raw/barcodes.tsv" barcodes.tsv mv "Solo.out/Gene/raw/features.tsv" features.tsv - mv "Solo.out/Gene/raw/matrix.mtx" matrix.mtx mv "Solo.out/Gene/CellReads.stats" CellReads.stats mv "Solo.out/Gene/Features.stats" Features.stats mv "Solo.out/Gene/Summary.csv" Summary.csv @@ -388,24 +392,33 @@ task STARsoloFastq { then if [[ "~{count_exons}" == "false" ]] then + SoloDirectory="Solo.out/GeneFull_Ex50pAS/raw" + echo "SoloDirectory is $SoloDirectory" + find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} echo mv {} /cromwell_root/ + find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/ mv "Solo.out/GeneFull_Ex50pAS/raw/barcodes.tsv" barcodes.tsv mv "Solo.out/GeneFull_Ex50pAS/raw/features.tsv" features.tsv - mv "Solo.out/GeneFull_Ex50pAS/raw/matrix.mtx" matrix.mtx mv "Solo.out/GeneFull_Ex50pAS/CellReads.stats" CellReads.stats mv "Solo.out/GeneFull_Ex50pAS/Features.stats" Features.stats mv "Solo.out/GeneFull_Ex50pAS/Summary.csv" Summary.csv mv "Solo.out/GeneFull_Ex50pAS/UMIperCellSorted.txt" UMIperCellSorted.txt else + SoloDirectory="Solo.out/GeneFull_Ex50pAS/raw" + echo "SoloDirectory is $SoloDirectory" + find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} echo mv {} /cromwell_root/ + find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} mv {} /cromwell_root/ + SoloDirectory="Solo.out/Gene/raw" + echo "SoloDirectory is $SoloDirectory" + find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} sh -c 'new_name="$(basename {} .mtx)_sn_rna.mtx"; echo mv {} "/cromwell_root/$new_name"' + find "$SoloDirectory" -maxdepth 1 -type f -name "*.mtx" -print0 | xargs -0 -I{} sh -c 'new_name="$(basename {} .mtx)_sn_rna.mtx"; mv {} "/cromwell_root/$new_name"' mv "Solo.out/GeneFull_Ex50pAS/raw/barcodes.tsv" barcodes.tsv mv "Solo.out/GeneFull_Ex50pAS/raw/features.tsv" features.tsv - mv "Solo.out/GeneFull_Ex50pAS/raw/matrix.mtx" matrix.mtx mv "Solo.out/GeneFull_Ex50pAS/CellReads.stats" CellReads.stats mv "Solo.out/GeneFull_Ex50pAS/Features.stats" Features.stats mv "Solo.out/GeneFull_Ex50pAS/Summary.csv" Summary.csv mv "Solo.out/GeneFull_Ex50pAS/UMIperCellSorted.txt" UMIperCellSorted.txt mv "Solo.out/Gene/raw/barcodes.tsv" barcodes_sn_rna.tsv mv "Solo.out/Gene/raw/features.tsv" features_sn_rna.tsv - mv "Solo.out/Gene/raw/matrix.mtx" matrix_sn_rna.mtx mv "Solo.out/Gene/CellReads.stats" CellReads_sn_rna.stats mv "Solo.out/Gene/Features.stats" Features_sn_rna.stats mv "Solo.out/Gene/Summary.csv" Summary_sn_rna.csv @@ -445,6 +458,10 @@ task STARsoloFastq { File align_features_sn_rna = "Features_sn_rna.stats" File summary_sn_rna = "Summary_sn_rna.csv" File umipercell_sn_rna = "UMIperCellSorted_sn_rna.txt" + File? multimappers_EM_matrix = "UniqueAndMult-EM.mtx" + File? multimappers_Uniform_matrix = "UniqueAndMult-Uniform.mtx" + File? multimappers_Rescue_matrix = "UniqueAndMult-Rescue.mtx" + File? multimappers_PropUnique_matrix = "UniqueAndMult-PropUnique.mtx" } } diff --git a/verification/test-wdls/TestMultiome.wdl b/verification/test-wdls/TestMultiome.wdl 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 } 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 diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md index 413e6addcf..3057f89507 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] | @@ -114,7 +115,11 @@ The Multiome workflow calls two WARP subworkflows, one external subworkflow (opt | gene_metrics_gex | `_gex.gene_metrics.csv.gz` | CSV file containing the per-gene metrics. | | cell_calls_gex | `_gex.emptyDrops` | TSV file containing the EmptyDrops results when the Optimus workflow is run in sc_rna mode. | | h5ad_output_file_gex | `_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. | -| cell_barcodes_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 | `` | 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 | `` | 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 | `` | 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 | `` | 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..71b18e89c5 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 +253,10 @@ The following table lists the output files produced from the pipeline. For sampl | cell_metrics | `.cell-metrics.csv.gz` | Matrix of metrics by cells. | Compressed CSV | | gene_metrics | `.gene-metrics.csv.gz` | Matrix of metrics by genes. | Compressed CSV | | aligner_metrics | `.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 | | cell_calls | empty_drops_result.csv | emptyDrops results from the RunEmptyDrops task. | CSV | | h5ad_output_file | `.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)