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biobox/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
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name: "bd_rhapsody_sequence_analysis"
namespace: "bd_rhapsody"
version: "main"
authors:
- name: "Robrecht Cannoodt"
roles:
- "author"
- "maintainer"
info:
links:
email: "robrecht@data-intuitive.com"
github: "rcannood"
orcid: "0000-0003-3641-729X"
linkedin: "robrechtcannoodt"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Science Engineer"
- name: "Open Problems"
href: "https://openproblems.bio"
role: "Core Member"
- name: "Weiwei Schultz"
roles:
- "contributor"
info:
organizations:
- name: "Janssen R&D US"
role: "Associate Director Data Sciences"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--reads"
description: "Reads (optional) - Path to your FASTQ.GZ formatted read files from\
\ libraries that may include:\n\n- WTA mRNA\n- Targeted mRNA\n- AbSeq\n- Sample\
\ Multiplexing\n- VDJ\n\nYou may specify as many R1/R2 read pairs as you want.\n"
info:
config_key: "Reads"
example:
- "WTALibrary_S1_L001_R1_001.fastq.gz"
- "WTALibrary_S1_L001_R2_001.fastq.gz"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--reads_atac"
description: "Path to your FASTQ.GZ formatted read files from ATAC-Seq libraries.\n\
You may specify as many R1/R2/I2 files as you want.\n"
info:
config_key: "Reads_ATAC"
example:
- "ATACLibrary_S2_L001_R1_001.fastq.gz"
- "ATACLibrary_S2_L001_R2_001.fastq.gz"
- "ATACLibrary_S2_L001_I2_001.fastq.gz"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: true
multiple_sep: ";"
- name: "References"
description: "Assay type will be inferred from the provided reference(s).\nDo not\
\ provide both reference_archive and targeted_reference at the same time.\n\n\
Valid reference input combinations:\n - reference_archive: WTA only\n - reference_archive\
\ & abseq_reference: WTA + AbSeq\n - reference_archive & supplemental_reference:\
\ WTA + extra transgenes\n - reference_archive & abseq_reference & supplemental_reference:\
\ WTA + AbSeq + extra transgenes\n - reference_archive: WTA + ATAC or ATAC only\n\
\ - reference_archive & supplemental_reference: WTA + ATAC + extra transgenes\n\
\ - targeted_reference: Targeted only\n - targeted_reference & abseq_reference:\
\ Targeted + AbSeq\n - abseq_reference: AbSeq only\n\nThe reference_archive can\
\ be generated with the bd_rhapsody_make_reference component.\nAlternatively,\
\ BD also provides standard references which can be downloaded from these locations:\n\
\n - Human: https://bd-rhapsody-public.s3.amazonaws.com/Rhapsody-WTA/Pipeline-version2.x_WTA_references/RhapRef_Human_WTA_2023-02.tar.gz\n\
\ - Mouse: https://bd-rhapsody-public.s3.amazonaws.com/Rhapsody-WTA/Pipeline-version2.x_WTA_references/RhapRef_Mouse_WTA_2023-02.tar.gz\n"
arguments:
- type: "file"
name: "--reference_archive"
description: "Path to Rhapsody WTA Reference in the tar.gz format.\n\nStructure\
\ of the reference archive:\n\n- `BD_Rhapsody_Reference_Files/`: top level folder\n\
\ - `star_index/`: sub-folder containing STAR index, that is files created\
\ with `STAR --runMode genomeGenerate`\n - GTF for gene-transcript-annotation\
\ e.g. \"gencode.v43.primary_assembly.annotation.gtf\"\n"
info:
config_key: "Reference_Archive"
example:
- "RhapRef_Human_WTA_2023-02.tar.gz"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--targeted_reference"
description: "Path to the targeted reference file in FASTA format.\n"
info:
config_key: "Targeted_Reference"
example:
- "BD_Rhapsody_Immune_Response_Panel_Hs.fasta"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--abseq_reference"
description: "Path to the AbSeq reference file in FASTA format. Only needed if\
\ BD AbSeq Ab-Oligos are used."
info:
config_key: "AbSeq_Reference"
example:
- "AbSeq_reference.fasta"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--supplemental_reference"
alternatives:
- "-s"
description: "Path to the supplemental reference file in FASTA format. Only needed\
\ if there are additional transgene sequences to be aligned against in a WTA\
\ assay experiment."
info:
config_key: "Supplemental_Reference"
example:
- "supplemental_reference.fasta"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: true
multiple_sep: ";"
- name: "Outputs"
description: "Outputs for all pipeline runs"
arguments:
- type: "file"
name: "--output_dir"
alternatives:
- "-o"
description: "The unprocessed output directory containing all the outputs from\
\ the pipeline."
info: null
example:
- "output_dir"
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--output_seurat"
description: "Single-cell analysis tool inputs. Seurat (.rds) input file containing\
\ RSEC molecules data table and all cell annotation metadata."
info:
template: "[sample_name]_Seurat.rds"
example:
- "output_seurat.rds"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--output_mudata"
description: "Single-cell analysis tool inputs. Scanpy / Muon input file containing\
\ RSEC molecules data table and all cell annotation metadata."
info:
template: "[sample_name].h5mu"
example:
- "output_mudata.h5mu"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--metrics_summary"
description: "Metrics Summary. Report containing sequencing, molecules, and cell\
\ metrics."
info:
template: "[sample_name]_Metrics_Summary.csv"
example:
- "metrics_summary.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pipeline_report"
description: "Pipeline Report. Summary report containing the results from the\
\ sequencing analysis pipeline run."
info:
template: "[sample_name]_Pipeline_Report.html"
example:
- "pipeline_report.html"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--rsec_mols_per_cell"
description: "Molecules per bioproduct per cell bassed on RSEC"
info:
template: "[sample_name]_RSEC_MolsPerCell_MEX.zip"
example:
- "RSEC_MolsPerCell_MEX.zip"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--dbec_mols_per_cell"
description: "Molecules per bioproduct per cell bassed on DBEC. DBEC data table\
\ is only output if the experiment includes targeted mRNA or AbSeq bioproducts."
info:
template: "[sample_name]_DBEC_MolsPerCell_MEX.zip"
example:
- "DBEC_MolsPerCell_MEX.zip"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--rsec_mols_per_cell_unfiltered"
description: "Unfiltered tables containing all cell labels with ≥10 reads."
info:
template: "[sample_name]_RSEC_MolsPerCell_Unfiltered_MEX.zip"
example:
- "RSEC_MolsPerCell_Unfiltered_MEX.zip"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--bam"
description: "Alignment file of R2 with associated R1 annotations for Bioproduct."
info:
template: "[sample_name]_Bioproduct.bam"
example:
- "BioProduct.bam"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--bam_index"
description: "Index file for the alignment file."
info:
template: "[sample_name]_Bioproduct.bam.bai"
example:
- "BioProduct.bam.bai"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--bioproduct_stats"
description: "Bioproduct Stats. Metrics from RSEC and DBEC Unique Molecular Identifier\
\ adjustment algorithms on a per-bioproduct basis."
info:
template: "[sample_name]_Bioproduct_Stats.csv"
example:
- "Bioproduct_Stats.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--dimred_tsne"
description: "t-SNE dimensionality reduction coordinates per cell index"
info:
template: "[sample_name]_(assay)_tSNE_coordinates.csv"
example:
- "tSNE_coordinates.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--dimred_umap"
description: "UMAP dimensionality reduction coordinates per cell index"
info:
template: "[sample_name]_(assay)_UMAP_coordinates.csv"
example:
- "UMAP_coordinates.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--immune_cell_classification"
description: "Immune Cell Classification. Cell type classification based on the\
\ expression of immune cell markers."
info:
template: "[sample_name]_(assay)_cell_type_experimental.csv"
example:
- "Immune_Cell_Classification.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Multiplex outputs"
description: "Outputs when multiplex option is selected"
arguments:
- type: "file"
name: "--sample_tag_metrics"
description: "Sample Tag Metrics. Metrics from the sample determination algorithm."
info:
template: "[sample_name]_Sample_Tag_Metrics.csv"
example:
- "Sample_Tag_Metrics.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--sample_tag_calls"
description: "Sample Tag Calls. Assigned Sample Tag for each putative cell"
info:
template: "[sample_name]_Sample_Tag_Calls.csv"
example:
- "Sample_Tag_Calls.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--sample_tag_counts"
description: "Sample Tag Counts. Separate data tables and metric summary for cells\
\ assigned to each sample tag. Note: For putative cells that could not be assigned\
\ a specific Sample Tag, a Multiplet_and_Undetermined.zip file is also output."
info:
template: "[sample_name]_Sample_Tag[number].zip"
example:
- "Sample_Tag1.zip"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--sample_tag_counts_unassigned"
description: "Sample Tag Counts Unassigned. Data table and metric summary for\
\ cells that could not be assigned a specific Sample Tag."
info:
template: "[sample_name]_Multiplet_and_Undetermined.zip"
example:
- "Multiplet_and_Undetermined.zip"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- name: "VDJ Outputs"
description: "Outputs when VDJ option selected"
arguments:
- type: "file"
name: "--vdj_metrics"
description: "VDJ Metrics. Overall metrics from the VDJ analysis."
info:
template: "[sample_name]_VDJ_Metrics.csv"
example:
- "VDJ_Metrics.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--vdj_per_cell"
description: "VDJ Per Cell. Cell specific read and molecule counts, VDJ gene segments,\
\ CDR3 sequences, paired chains, and cell type."
info:
template: "[sample_name]_VDJ_perCell.csv"
example:
- "VDJ_perCell.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--vdj_per_cell_uncorrected"
description: "VDJ Per Cell Uncorrected. Cell specific read and molecule counts,\
\ VDJ gene segments, CDR3 sequences, paired chains, and cell type."
info:
template: "[sample_name]_VDJ_perCell_uncorrected.csv"
example:
- "VDJ_perCell_uncorrected.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--vdj_dominant_contigs"
description: "VDJ Dominant Contigs. Dominant contig for each cell label chain\
\ type combination (putative cells only)."
info:
template: "[sample_name]_VDJ_Dominant_Contigs_AIRR.csv"
example:
- "VDJ_Dominant_Contigs_AIRR.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--vdj_unfiltered_contigs"
description: "VDJ Unfiltered Contigs. All contigs that were assembled and annotated\
\ successfully (all cells)."
info:
template: "[sample_name]_VDJ_Unfiltered_Contigs_AIRR.csv"
example:
- "VDJ_Unfiltered_Contigs_AIRR.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- name: "ATAC-Seq outputs"
description: "Outputs when ATAC-Seq option selected"
arguments:
- type: "file"
name: "--atac_metrics"
description: "ATAC Metrics. Overall metrics from the ATAC-Seq analysis."
info:
template: "[sample_name]_ATAC_Metrics.csv"
example:
- "ATAC_Metrics.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--atac_metrics_json"
description: "ATAC Metrics JSON. Overall metrics from the ATAC-Seq analysis in\
\ JSON format."
info:
template: "[sample_name]_ATAC_Metrics.json"
example:
- "ATAC_Metrics.json"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--atac_fragments"
description: "ATAC Fragments. Chromosomal location, cell index, and read support\
\ for each fragment detected"
info:
template: "[sample_name]_ATAC_Fragments.bed.gz"
example:
- "ATAC_Fragments.bed.gz"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--atac_fragments_index"
description: "Index of ATAC Fragments."
info:
template: "[sample_name]_ATAC_Fragments.bed.gz.tbi"
example:
- "ATAC_Fragments.bed.gz.tbi"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--atac_transposase_sites"
description: "ATAC Transposase Sites. Chromosomal location, cell index, and read\
\ support for each transposase site detected"
info:
template: "[sample_name]_ATAC_Transposase_Sites.bed.gz"
example:
- "ATAC_Transposase_Sites.bed.gz"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--atac_transposase_sites_index"
description: "Index of ATAC Transposase Sites."
info:
template: "[sample_name]_ATAC_Transposase_Sites.bed.gz.tbi"
example:
- "ATAC_Transposase_Sites.bed.gz.tbi"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--atac_peaks"
description: "ATAC Peaks. Peak regions of transposase activity"
info:
template: "[sample_name]_ATAC_Peaks.bed.gz"
example:
- "ATAC_Peaks.bed.gz"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--atac_peaks_index"
description: "Index of ATAC Peaks."
info:
template: "[sample_name]_ATAC_Peaks.bed.gz.tbi"
example:
- "ATAC_Peaks.bed.gz.tbi"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--atac_peak_annotation"
description: "ATAC Peak Annotation. Estimated annotation of peak-to-gene connections"
info:
template: "[sample_name]_peak_annotation.tsv.gz"
example:
- "peak_annotation.tsv.gz"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--atac_cell_by_peak"
description: "ATAC Cell by Peak. Peak regions of transposase activity per cell"
info:
template: "[sample_name]_ATAC_Cell_by_Peak_MEX.zip"
example:
- "ATAC_Cell_by_Peak_MEX.zip"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--atac_cell_by_peak_unfiltered"
description: "ATAC Cell by Peak Unfiltered. Unfiltered file containing all cell\
\ labels with >=1 transposase sites in peaks."
info:
template: "[sample_name]_ATAC_Cell_by_Peak_Unfiltered_MEX.zip"
example:
- "ATAC_Cell_by_Peak_Unfiltered_MEX.zip"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--atac_bam"
description: "ATAC BAM. Alignment file for R1 and R2 with associated I2 annotations\
\ for ATAC-Seq. Only output if the BAM generation flag is set to true."
info:
template: "[sample_name]_ATAC.bam"
example:
- "ATAC.bam"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--atac_bam_index"
description: "Index of ATAC BAM."
info:
template: "[sample_name]_ATAC.bam.bai"
example:
- "ATAC.bam.bai"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- name: "AbSeq Cell Calling outputs"
description: "Outputs when Cell Calling Abseq is selected"
arguments:
- type: "file"
name: "--protein_aggregates_experimental"
description: "Protein Aggregates Experimental"
info:
template: "[sample_name]_Protein_Aggregates_Experimental.csv"
example:
- "Protein_Aggregates_Experimental.csv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Putative Cell Calling Settings"
arguments:
- type: "string"
name: "--cell_calling_data"
description: "Specify the dataset to be used for putative cell calling: mRNA,\
\ AbSeq, ATAC, mRNA_and_ATAC\n\nFor putative cell calling using an AbSeq dataset,\
\ please provide an AbSeq_Reference fasta file above.\n\nFor putative cell calling\
\ using an ATAC dataset, please provide a WTA+ATAC-Seq Reference_Archive file\
\ above.\n\nThe default data for putative cell calling, will be determined the\
\ following way:\n\n- If mRNA Reads and ATAC Reads exist: mRNA_and_ATAC\n- If\
\ only ATAC Reads exist: ATAC\n- Otherwise: mRNA\n"
info:
config_key: "Cell_Calling_Data"
example:
- "mRNA"
required: false
choices:
- "mRNA"
- "AbSeq"
- "ATAC"
- "mRNA_and_ATAC"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--cell_calling_bioproduct_algorithm"
description: "Specify the bioproduct algorithm to be used for putative cell calling:\
\ Basic or Refined\n\nBy default, the Basic algorithm will be used for putative\
\ cell calling.\n"
info:
config_key: "Cell_Calling_Bioproduct_Algorithm"
example:
- "Basic"
required: false
choices:
- "Basic"
- "Refined"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--cell_calling_atac_algorithm"
description: "Specify the ATAC-seq algorithm to be used for putative cell calling:\
\ Basic or Refined\n\nBy default, the Basic algorithm will be used for putative\
\ cell calling.\n"
info:
config_key: "Cell_Calling_ATAC_Algorithm"
example:
- "Basic"
required: false
choices:
- "Basic"
- "Refined"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--exact_cell_count"
description: "Set a specific number (>=1) of cells as putative, based on those\
\ with the highest error-corrected read count\n"
info:
config_key: "Exact_Cell_Count"
example:
- 10000
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--expected_cell_count"
description: "Guide the basic putative cell calling algorithm by providing an\
\ estimate of the number of cells expected. Usually this can be the number\
\ of cells loaded into the Rhapsody cartridge. If there are multiple inflection\
\ points on the second derivative cumulative curve, this will ensure the one\
\ selected is near the expected. \n"
info:
config_key: "Expected_Cell_Count"
example:
- 20000
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Intronic Reads Settings"
arguments:
- type: "boolean"
name: "--exclude_intronic_reads"
description: "By default, the flag is false, and reads aligned to exons and introns\
\ are considered and represented in molecule counts. When the flag is set to\
\ true, intronic reads will be excluded.\nThe value can be true or false.\n"
info:
config_key: "Exclude_Intronic_Reads"
example:
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Multiplex Settings"
arguments:
- type: "string"
name: "--sample_tags_version"
description: "Specify the version of the Sample Tags used in the run:\n\n* If\
\ Sample Tag Multiplexing was done, specify the appropriate version: human,\
\ mouse, flex, nuclei_includes_mrna, nuclei_atac_only\n* If this is an SMK +\
\ Nuclei mRNA run or an SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq) run (and not\
\ an SMK + ATAC-Seq only run), choose the \"nuclei_includes_mrna\" option.\n\
* If this is an SMK + ATAC-Seq only run (and not SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq)),\
\ choose the \"nuclei_atac_only\" option.\n"
info:
config_key: "Sample_Tags_Version"
example:
- "human"
required: false
choices:
- "human"
- "mouse"
- "flex"
- "nuclei_includes_mrna"
- "nuclei_atac_only"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--tag_names"
description: "Specify the tag number followed by '-' and the desired sample name\
\ to appear in Sample_Tag_Metrics.csv\nDo not use the special characters: &,\
\ (), [], {}, <>, ?, |\n"
info:
config_key: "Tag_Names"
example:
- "4-mySample"
- "9-myOtherSample"
- "6-alsoThisSample"
required: false
direction: "input"
multiple: true
multiple_sep: ";"
- name: "VDJ arguments"
arguments:
- type: "string"
name: "--vdj_version"
description: "If VDJ was done, specify the appropriate option: human, mouse, humanBCR,\
\ humanTCR, mouseBCR, mouseTCR\n"
info:
config_key: "VDJ_Version"
example:
- "human"
required: false
choices:
- "human"
- "mouse"
- "humanBCR"
- "humanTCR"
- "mouseBCR"
- "mouseTCR"
direction: "input"
multiple: false
multiple_sep: ";"
- name: "ATAC options"
arguments:
- type: "file"
name: "--predefined_atac_peaks"
description: "An optional BED file containing pre-established chromatin accessibility\
\ peak regions for generating the ATAC cell-by-peak matrix."
info:
config_key: "Predefined_ATAC_Peaks"
example:
- "predefined_peaks.bed"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Additional options"
arguments:
- type: "string"
name: "--run_name"
description: "Specify a run name to use as the output file base name. Use only\
\ letters, numbers, or hyphens. Do not use special characters or spaces.\n"
info:
config_key: "Run_Name"
default:
- "sample"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--generate_bam"
description: "Specify whether to create the BAM file output\n"
info:
config_key: "Generate_Bam"
default:
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--long_reads"
description: "Use STARlong (default: undefined - i.e. autodetects based on read\
\ lengths) - Specify if the STARlong aligner should be used instead of STAR.\
\ Set to true if the reads are longer than 650bp.\n"
info:
config_key: "Long_Reads"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Advanced options"
description: "NOTE: Only change these if you are really sure about what you are\
\ doing\n"
arguments:
- type: "string"
name: "--custom_star_params"
description: "Modify STAR alignment parameters - Set this parameter to fully override\
\ default STAR mapping parameters used in the pipeline.\nFor reference this\
\ is the default that is used:\n\n Short Reads: `--outFilterScoreMinOverLread\
\ 0 --outFilterMatchNminOverLread 0 --outFilterMultimapScoreRange 0 --clip3pAdapterSeq\
\ AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA --seedSearchStartLmax 50 --outFilterMatchNmin\
\ 25 --limitOutSJcollapsed 2000000`\n Long Reads: Same as Short Reads + `--seedPerReadNmax\
\ 10000`\n\nThis applies to fastqs provided in the Reads user input \nDo NOT\
\ set any non-mapping related params like `--genomeDir`, `--outSAMtype`, `--outSAMunmapped`,\
\ `--readFilesIn`, `--runThreadN`, etc.\nWe use STAR version 2.7.10b\n"
info:
config_key: "Custom_STAR_Params"
example:
- "--alignIntronMax 6000 --outFilterScoreMinOverLread 0.1 --limitOutSJcollapsed\
\ 2000000"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--custom_bwa_mem2_params"
description: "Modify bwa-mem2 alignment parameters - Set this parameter to fully\
\ override bwa-mem2 mapping parameters used in the pipeline\nThe pipeline does\
\ not specify any custom mapping params to bwa-mem2 so program default values\
\ are used\nThis applies to fastqs provided in the Reads_ATAC user input \n\
Do NOT set any non-mapping related params like `-C`, `-t`, etc.\nWe use bwa-mem2\
\ version 2.2.1\n"
info:
config_key: "Custom_bwa_mem2_Params"
example:
- "-k 16 -w 200 -r"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "CWL-runner arguments"
arguments:
- type: "boolean"
name: "--parallel"
description: "Run jobs in parallel."
info: null
default:
- true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--timestamps"
description: "Add timestamps to the errors, warnings, and notifications."
info: null
direction: "input"
- name: "Undocumented arguments"
arguments:
- type: "integer"
name: "--abseq_umi"
info:
config_key: "AbSeq_UMI"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--target_analysis"
info:
config_key: "Target_analysis"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--vdj_jgene_evalue"
description: "e-value threshold for J gene. The e-value threshold for J gene call\
\ by IgBlast/PyIR, default is set as 0.001\n"
info:
config_key: "VDJ_JGene_Evalue"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--vdj_vgene_evalue"
description: "e-value threshold for V gene. The e-value threshold for V gene call\
\ by IgBlast/PyIR, default is set as 0.001\n"
info:
config_key: "VDJ_VGene_Evalue"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--write_filtered_reads"
info:
config_key: "Write_Filtered_Reads"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
resources:
- type: "python_script"
path: "script.py"
is_executable: true
description: "BD Rhapsody Sequence Analysis CWL pipeline v2.2.\n\nThis pipeline performs\
\ analysis of single-cell multiomic sequence read (FASTQ) data. The supported\n\
sequencing libraries are those generated by the BD Rhapsody™ assay kits, including:\
\ Whole Transcriptome\nmRNA (WTA), Targeted mRNA, AbSeq Antibody-Oligonucleotides\
\ (ABC), Single-Cell Multiplexing (SMK),\nTCR/BCR (VDJ), and ATAC-Seq.\n"
test_resources:
- type: "python_script"
path: "test.py"
is_executable: true
- type: "file"
path: "test_data"
- type: "file"
path: "helpers"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
keywords:
- "rna-seq"
- "single-cell"
- "multiomic"
- "atac-seq"
- "targeted"
- "abseq"
- "tcr"
- "bcr"
license: "Unknown"
links:
repository: "https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1"
documentation: "https://bd-rhapsody-bioinfo-docs.genomics.bd.com"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "bdgenomics/rhapsody:2.2.1"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "procps"
- "git"
interactive: false
- type: "python"
user: false
packages:
- "cwlref-runner"
- "cwl-runner"
upgrade: true
- type: "docker"
run:
- "mkdir /var/bd_rhapsody_cwl && \\\n cd /var/bd_rhapsody_cwl && \\\n git clone\
\ https://bitbucket.org/CRSwDev/cwl.git . && \\\n git checkout 8feeace1141b24749ea6003f8e6ad6d3ad5232de\n"
- type: "docker"
run:
- "VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)"
- "echo \"bdgenomics/rhapsody: \\\"$VERSION\\\"\" > /var/software_versions.txt"
test_setup:
- type: "python"
user: false
packages:
- "biopython"
- "gffutils"
upgrade: true
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/bd_rhapsody/bd_rhapsody_sequence_analysis/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis"
executable: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis"
viash_version: "0.9.4"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"
- "sequencing"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/biobox"
issue_tracker: "https://github.com/viash-hub/biobox/issues"
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