{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "bd_rhapsody_sequence_analysis",
"description": "BD Rhapsody Sequence Analysis CWL pipeline v2.2.\n\nThis pipeline performs analysis of single-cell multiomic sequence read (FASTQ) data. The supported\nsequencing libraries are those generated by the BD Rhapsody\u2122 assay kits, including: Whole Transcriptome\nmRNA (WTA), Targeted mRNA, AbSeq Antibody-Oligonucleotides (ABC), Single-Cell Multiplexing (SMK),\nTCR/BCR (VDJ), and ATAC-Seq.\n",
"type": "object",
"definitions": {

    
    
    "inputs" : {
    "title": "Inputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "reads": {
                "type":
                "string",
                "description": "Type: List of `file`, example: `WTALibrary_S1_L001_R1_001.fastq.gz;WTALibrary_S1_L001_R2_001.fastq.gz`, multiple_sep: `\";\"`. Reads (optional) - Path to your FASTQ",
                "help_text": "Type: List of `file`, example: `WTALibrary_S1_L001_R1_001.fastq.gz;WTALibrary_S1_L001_R2_001.fastq.gz`, multiple_sep: `\";\"`. 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"
            
            }
    

        ,
                "reads_atac": {
                "type":
                "string",
                "description": "Type: List of `file`, example: `ATACLibrary_S2_L001_R1_001.fastq.gz;ATACLibrary_S2_L001_R2_001.fastq.gz;ATACLibrary_S2_L001_I2_001.fastq.gz`, multiple_sep: `\";\"`. Path to your FASTQ",
                "help_text": "Type: List of `file`, example: `ATACLibrary_S2_L001_R1_001.fastq.gz;ATACLibrary_S2_L001_R2_001.fastq.gz;ATACLibrary_S2_L001_I2_001.fastq.gz`, multiple_sep: `\";\"`. Path to your FASTQ.GZ formatted read files from ATAC-Seq libraries.\nYou may specify as many R1/R2/I2 files as you want.\n"
            
            }
    

}
},
    
    
    "outputs" : {
    "title": "Outputs",
    "type": "object",
    "description": "Outputs for all pipeline runs",
    "properties": {
    
        
                "output_dir": {
                "type":
                "string",
                "description": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`, example: `output_dir`. The unprocessed output directory containing all the outputs from the pipeline",
                "help_text": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`, example: `output_dir`. The unprocessed output directory containing all the outputs from the pipeline."
            ,
                "default": "$id.$key.output_dir.output_dir"
            }
    

        ,
                "output_seurat": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_seurat.rds`, example: `output_seurat.rds`. Single-cell analysis tool inputs",
                "help_text": "Type: `file`, default: `$id.$key.output_seurat.rds`, example: `output_seurat.rds`. Single-cell analysis tool inputs. Seurat (.rds) input file containing RSEC molecules data table and all cell annotation metadata."
            ,
                "default": "$id.$key.output_seurat.rds"
            }
    

        ,
                "output_mudata": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_mudata.h5mu`, example: `output_mudata.h5mu`. Single-cell analysis tool inputs",
                "help_text": "Type: `file`, default: `$id.$key.output_mudata.h5mu`, example: `output_mudata.h5mu`. Single-cell analysis tool inputs. Scanpy / Muon input file containing RSEC molecules data table and all cell annotation metadata."
            ,
                "default": "$id.$key.output_mudata.h5mu"
            }
    

        ,
                "metrics_summary": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.metrics_summary.csv`, example: `metrics_summary.csv`. Metrics Summary",
                "help_text": "Type: `file`, default: `$id.$key.metrics_summary.csv`, example: `metrics_summary.csv`. Metrics Summary. Report containing sequencing, molecules, and cell metrics."
            ,
                "default": "$id.$key.metrics_summary.csv"
            }
    

        ,
                "pipeline_report": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.pipeline_report.html`, example: `pipeline_report.html`. Pipeline Report",
                "help_text": "Type: `file`, default: `$id.$key.pipeline_report.html`, example: `pipeline_report.html`. Pipeline Report. Summary report containing the results from the sequencing analysis pipeline run."
            ,
                "default": "$id.$key.pipeline_report.html"
            }
    

        ,
                "rsec_mols_per_cell": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.rsec_mols_per_cell.zip`, example: `RSEC_MolsPerCell_MEX.zip`. Molecules per bioproduct per cell bassed on RSEC",
                "help_text": "Type: `file`, default: `$id.$key.rsec_mols_per_cell.zip`, example: `RSEC_MolsPerCell_MEX.zip`. Molecules per bioproduct per cell bassed on RSEC"
            ,
                "default": "$id.$key.rsec_mols_per_cell.zip"
            }
    

        ,
                "dbec_mols_per_cell": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.dbec_mols_per_cell.zip`, example: `DBEC_MolsPerCell_MEX.zip`. Molecules per bioproduct per cell bassed on DBEC",
                "help_text": "Type: `file`, default: `$id.$key.dbec_mols_per_cell.zip`, example: `DBEC_MolsPerCell_MEX.zip`. Molecules per bioproduct per cell bassed on DBEC. DBEC data table is only output if the experiment includes targeted mRNA or AbSeq bioproducts."
            ,
                "default": "$id.$key.dbec_mols_per_cell.zip"
            }
    

        ,
                "rsec_mols_per_cell_unfiltered": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.rsec_mols_per_cell_unfiltered.zip`, example: `RSEC_MolsPerCell_Unfiltered_MEX.zip`. Unfiltered tables containing all cell labels with \u226510 reads",
                "help_text": "Type: `file`, default: `$id.$key.rsec_mols_per_cell_unfiltered.zip`, example: `RSEC_MolsPerCell_Unfiltered_MEX.zip`. Unfiltered tables containing all cell labels with \u226510 reads."
            ,
                "default": "$id.$key.rsec_mols_per_cell_unfiltered.zip"
            }
    

        ,
                "bam": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.bam.bam`, example: `BioProduct.bam`. Alignment file of R2 with associated R1 annotations for Bioproduct",
                "help_text": "Type: `file`, default: `$id.$key.bam.bam`, example: `BioProduct.bam`. Alignment file of R2 with associated R1 annotations for Bioproduct."
            ,
                "default": "$id.$key.bam.bam"
            }
    

        ,
                "bam_index": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.bam_index.bai`, example: `BioProduct.bam.bai`. Index file for the alignment file",
                "help_text": "Type: `file`, default: `$id.$key.bam_index.bai`, example: `BioProduct.bam.bai`. Index file for the alignment file."
            ,
                "default": "$id.$key.bam_index.bai"
            }
    

        ,
                "bioproduct_stats": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.bioproduct_stats.csv`, example: `Bioproduct_Stats.csv`. Bioproduct Stats",
                "help_text": "Type: `file`, default: `$id.$key.bioproduct_stats.csv`, example: `Bioproduct_Stats.csv`. Bioproduct Stats. Metrics from RSEC and DBEC Unique Molecular Identifier adjustment algorithms on a per-bioproduct basis."
            ,
                "default": "$id.$key.bioproduct_stats.csv"
            }
    

        ,
                "dimred_tsne": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.dimred_tsne.csv`, example: `tSNE_coordinates.csv`. t-SNE dimensionality reduction coordinates per cell index",
                "help_text": "Type: `file`, default: `$id.$key.dimred_tsne.csv`, example: `tSNE_coordinates.csv`. t-SNE dimensionality reduction coordinates per cell index"
            ,
                "default": "$id.$key.dimred_tsne.csv"
            }
    

        ,
                "dimred_umap": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.dimred_umap.csv`, example: `UMAP_coordinates.csv`. UMAP dimensionality reduction coordinates per cell index",
                "help_text": "Type: `file`, default: `$id.$key.dimred_umap.csv`, example: `UMAP_coordinates.csv`. UMAP dimensionality reduction coordinates per cell index"
            ,
                "default": "$id.$key.dimred_umap.csv"
            }
    

        ,
                "immune_cell_classification": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.immune_cell_classification.csv`, example: `Immune_Cell_Classification.csv`. Immune Cell Classification",
                "help_text": "Type: `file`, default: `$id.$key.immune_cell_classification.csv`, example: `Immune_Cell_Classification.csv`. Immune Cell Classification. Cell type classification based on the expression of immune cell markers."
            ,
                "default": "$id.$key.immune_cell_classification.csv"
            }
    

}
},
    
    
    "references" : {
    "title": "References",
    "type": "object",
    "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\nValid reference input combinations:\n  - reference_archive: WTA only\n  - reference_archive \u0026 abseq_reference: WTA + AbSeq\n  - reference_archive \u0026 supplemental_reference: WTA + extra transgenes\n  - reference_archive \u0026 abseq_reference \u0026 supplemental_reference: WTA + AbSeq + extra transgenes\n  - reference_archive: WTA + ATAC or ATAC only\n  - reference_archive \u0026 supplemental_reference: WTA + ATAC + extra transgenes\n  - targeted_reference: Targeted only\n  - targeted_reference \u0026 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",
    "properties": {
    
        
                "reference_archive": {
                "type":
                "string",
                "description": "Type: `file`, example: `RhapRef_Human_WTA_2023-02.tar.gz`. Path to Rhapsody WTA Reference in the tar",
                "help_text": "Type: `file`, example: `RhapRef_Human_WTA_2023-02.tar.gz`. 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"
            
            }
    

        ,
                "targeted_reference": {
                "type":
                "string",
                "description": "Type: List of `file`, example: `BD_Rhapsody_Immune_Response_Panel_Hs.fasta`, multiple_sep: `\";\"`. Path to the targeted reference file in FASTA format",
                "help_text": "Type: List of `file`, example: `BD_Rhapsody_Immune_Response_Panel_Hs.fasta`, multiple_sep: `\";\"`. Path to the targeted reference file in FASTA format.\n"
            
            }
    

        ,
                "abseq_reference": {
                "type":
                "string",
                "description": "Type: List of `file`, example: `AbSeq_reference.fasta`, multiple_sep: `\";\"`. Path to the AbSeq reference file in FASTA format",
                "help_text": "Type: List of `file`, example: `AbSeq_reference.fasta`, multiple_sep: `\";\"`. Path to the AbSeq reference file in FASTA format.  Only needed if BD AbSeq Ab-Oligos are used."
            
            }
    

        ,
                "supplemental_reference": {
                "type":
                "string",
                "description": "Type: List of `file`, example: `supplemental_reference.fasta`, multiple_sep: `\";\"`. Path to the supplemental reference file in FASTA format",
                "help_text": "Type: List of `file`, example: `supplemental_reference.fasta`, multiple_sep: `\";\"`. 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."
            
            }
    

}
},
    
    
    "multiplex outputs" : {
    "title": "Multiplex outputs",
    "type": "object",
    "description": "Outputs when multiplex option is selected",
    "properties": {
    
        
                "sample_tag_metrics": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.sample_tag_metrics.csv`, example: `Sample_Tag_Metrics.csv`. Sample Tag Metrics",
                "help_text": "Type: `file`, default: `$id.$key.sample_tag_metrics.csv`, example: `Sample_Tag_Metrics.csv`. Sample Tag Metrics. Metrics from the sample determination algorithm."
            ,
                "default": "$id.$key.sample_tag_metrics.csv"
            }
    

        ,
                "sample_tag_calls": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.sample_tag_calls.csv`, example: `Sample_Tag_Calls.csv`. Sample Tag Calls",
                "help_text": "Type: `file`, default: `$id.$key.sample_tag_calls.csv`, example: `Sample_Tag_Calls.csv`. Sample Tag Calls. Assigned Sample Tag for each putative cell"
            ,
                "default": "$id.$key.sample_tag_calls.csv"
            }
    

        ,
                "sample_tag_counts": {
                "type":
                "string",
                "description": "Type: List of `file`, default: `$id.$key.sample_tag_counts_*.zip`, example: `Sample_Tag1.zip`, multiple_sep: `\";\"`. Sample Tag Counts",
                "help_text": "Type: List of `file`, default: `$id.$key.sample_tag_counts_*.zip`, example: `Sample_Tag1.zip`, multiple_sep: `\";\"`. 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."
            ,
                "default": "$id.$key.sample_tag_counts_*.zip"
            }
    

        ,
                "sample_tag_counts_unassigned": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.sample_tag_counts_unassigned.zip`, example: `Multiplet_and_Undetermined.zip`. Sample Tag Counts Unassigned",
                "help_text": "Type: `file`, default: `$id.$key.sample_tag_counts_unassigned.zip`, example: `Multiplet_and_Undetermined.zip`. Sample Tag Counts Unassigned. Data table and metric summary for cells that could not be assigned a specific Sample Tag."
            ,
                "default": "$id.$key.sample_tag_counts_unassigned.zip"
            }
    

}
},
    
    
    "vdj outputs" : {
    "title": "VDJ Outputs",
    "type": "object",
    "description": "Outputs when VDJ option selected",
    "properties": {
    
        
                "vdj_metrics": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.vdj_metrics.csv`, example: `VDJ_Metrics.csv`. VDJ Metrics",
                "help_text": "Type: `file`, default: `$id.$key.vdj_metrics.csv`, example: `VDJ_Metrics.csv`. VDJ Metrics. Overall metrics from the VDJ analysis."
            ,
                "default": "$id.$key.vdj_metrics.csv"
            }
    

        ,
                "vdj_per_cell": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.vdj_per_cell.csv`, example: `VDJ_perCell.csv`. VDJ Per Cell",
                "help_text": "Type: `file`, default: `$id.$key.vdj_per_cell.csv`, example: `VDJ_perCell.csv`. VDJ Per Cell. Cell specific read and molecule counts, VDJ gene segments, CDR3 sequences, paired chains, and cell type."
            ,
                "default": "$id.$key.vdj_per_cell.csv"
            }
    

        ,
                "vdj_per_cell_uncorrected": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.vdj_per_cell_uncorrected.csv`, example: `VDJ_perCell_uncorrected.csv`. VDJ Per Cell Uncorrected",
                "help_text": "Type: `file`, default: `$id.$key.vdj_per_cell_uncorrected.csv`, example: `VDJ_perCell_uncorrected.csv`. VDJ Per Cell Uncorrected. Cell specific read and molecule counts, VDJ gene segments, CDR3 sequences, paired chains, and cell type."
            ,
                "default": "$id.$key.vdj_per_cell_uncorrected.csv"
            }
    

        ,
                "vdj_dominant_contigs": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.vdj_dominant_contigs.csv`, example: `VDJ_Dominant_Contigs_AIRR.csv`. VDJ Dominant Contigs",
                "help_text": "Type: `file`, default: `$id.$key.vdj_dominant_contigs.csv`, example: `VDJ_Dominant_Contigs_AIRR.csv`. VDJ Dominant Contigs. Dominant contig for each cell label chain type combination (putative cells only)."
            ,
                "default": "$id.$key.vdj_dominant_contigs.csv"
            }
    

        ,
                "vdj_unfiltered_contigs": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.vdj_unfiltered_contigs.csv`, example: `VDJ_Unfiltered_Contigs_AIRR.csv`. VDJ Unfiltered Contigs",
                "help_text": "Type: `file`, default: `$id.$key.vdj_unfiltered_contigs.csv`, example: `VDJ_Unfiltered_Contigs_AIRR.csv`. VDJ Unfiltered Contigs. All contigs that were assembled and annotated successfully (all cells)."
            ,
                "default": "$id.$key.vdj_unfiltered_contigs.csv"
            }
    

}
},
    
    
    "atac-seq outputs" : {
    "title": "ATAC-Seq outputs",
    "type": "object",
    "description": "Outputs when ATAC-Seq option selected",
    "properties": {
    
        
                "atac_metrics": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_metrics.csv`, example: `ATAC_Metrics.csv`. ATAC Metrics",
                "help_text": "Type: `file`, default: `$id.$key.atac_metrics.csv`, example: `ATAC_Metrics.csv`. ATAC Metrics. Overall metrics from the ATAC-Seq analysis."
            ,
                "default": "$id.$key.atac_metrics.csv"
            }
    

        ,
                "atac_metrics_json": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_metrics_json.json`, example: `ATAC_Metrics.json`. ATAC Metrics JSON",
                "help_text": "Type: `file`, default: `$id.$key.atac_metrics_json.json`, example: `ATAC_Metrics.json`. ATAC Metrics JSON. Overall metrics from the ATAC-Seq analysis in JSON format."
            ,
                "default": "$id.$key.atac_metrics_json.json"
            }
    

        ,
                "atac_fragments": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_fragments.gz`, example: `ATAC_Fragments.bed.gz`. ATAC Fragments",
                "help_text": "Type: `file`, default: `$id.$key.atac_fragments.gz`, example: `ATAC_Fragments.bed.gz`. ATAC Fragments. Chromosomal location, cell index, and read support for each fragment detected"
            ,
                "default": "$id.$key.atac_fragments.gz"
            }
    

        ,
                "atac_fragments_index": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_fragments_index.tbi`, example: `ATAC_Fragments.bed.gz.tbi`. Index of ATAC Fragments",
                "help_text": "Type: `file`, default: `$id.$key.atac_fragments_index.tbi`, example: `ATAC_Fragments.bed.gz.tbi`. Index of ATAC Fragments."
            ,
                "default": "$id.$key.atac_fragments_index.tbi"
            }
    

        ,
                "atac_transposase_sites": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_transposase_sites.gz`, example: `ATAC_Transposase_Sites.bed.gz`. ATAC Transposase Sites",
                "help_text": "Type: `file`, default: `$id.$key.atac_transposase_sites.gz`, example: `ATAC_Transposase_Sites.bed.gz`. ATAC Transposase Sites. Chromosomal location, cell index, and read support for each transposase site detected"
            ,
                "default": "$id.$key.atac_transposase_sites.gz"
            }
    

        ,
                "atac_transposase_sites_index": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_transposase_sites_index.tbi`, example: `ATAC_Transposase_Sites.bed.gz.tbi`. Index of ATAC Transposase Sites",
                "help_text": "Type: `file`, default: `$id.$key.atac_transposase_sites_index.tbi`, example: `ATAC_Transposase_Sites.bed.gz.tbi`. Index of ATAC Transposase Sites."
            ,
                "default": "$id.$key.atac_transposase_sites_index.tbi"
            }
    

        ,
                "atac_peaks": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_peaks.gz`, example: `ATAC_Peaks.bed.gz`. ATAC Peaks",
                "help_text": "Type: `file`, default: `$id.$key.atac_peaks.gz`, example: `ATAC_Peaks.bed.gz`. ATAC Peaks. Peak regions of transposase activity"
            ,
                "default": "$id.$key.atac_peaks.gz"
            }
    

        ,
                "atac_peaks_index": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_peaks_index.tbi`, example: `ATAC_Peaks.bed.gz.tbi`. Index of ATAC Peaks",
                "help_text": "Type: `file`, default: `$id.$key.atac_peaks_index.tbi`, example: `ATAC_Peaks.bed.gz.tbi`. Index of ATAC Peaks."
            ,
                "default": "$id.$key.atac_peaks_index.tbi"
            }
    

        ,
                "atac_peak_annotation": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_peak_annotation.gz`, example: `peak_annotation.tsv.gz`. ATAC Peak Annotation",
                "help_text": "Type: `file`, default: `$id.$key.atac_peak_annotation.gz`, example: `peak_annotation.tsv.gz`. ATAC Peak Annotation. Estimated annotation of peak-to-gene connections"
            ,
                "default": "$id.$key.atac_peak_annotation.gz"
            }
    

        ,
                "atac_cell_by_peak": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_cell_by_peak.zip`, example: `ATAC_Cell_by_Peak_MEX.zip`. ATAC Cell by Peak",
                "help_text": "Type: `file`, default: `$id.$key.atac_cell_by_peak.zip`, example: `ATAC_Cell_by_Peak_MEX.zip`. ATAC Cell by Peak. Peak regions of transposase activity per cell"
            ,
                "default": "$id.$key.atac_cell_by_peak.zip"
            }
    

        ,
                "atac_cell_by_peak_unfiltered": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_cell_by_peak_unfiltered.zip`, example: `ATAC_Cell_by_Peak_Unfiltered_MEX.zip`. ATAC Cell by Peak Unfiltered",
                "help_text": "Type: `file`, default: `$id.$key.atac_cell_by_peak_unfiltered.zip`, example: `ATAC_Cell_by_Peak_Unfiltered_MEX.zip`. ATAC Cell by Peak Unfiltered. Unfiltered file containing all cell labels with \u003e=1 transposase sites in peaks."
            ,
                "default": "$id.$key.atac_cell_by_peak_unfiltered.zip"
            }
    

        ,
                "atac_bam": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_bam.bam`, example: `ATAC.bam`. ATAC BAM",
                "help_text": "Type: `file`, default: `$id.$key.atac_bam.bam`, example: `ATAC.bam`. 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."
            ,
                "default": "$id.$key.atac_bam.bam"
            }
    

        ,
                "atac_bam_index": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.atac_bam_index.bai`, example: `ATAC.bam.bai`. Index of ATAC BAM",
                "help_text": "Type: `file`, default: `$id.$key.atac_bam_index.bai`, example: `ATAC.bam.bai`. Index of ATAC BAM."
            ,
                "default": "$id.$key.atac_bam_index.bai"
            }
    

}
},
    
    
    "abseq cell calling outputs" : {
    "title": "AbSeq Cell Calling outputs",
    "type": "object",
    "description": "Outputs when Cell Calling Abseq is selected",
    "properties": {
    
        
                "protein_aggregates_experimental": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.protein_aggregates_experimental.csv`, example: `Protein_Aggregates_Experimental.csv`. Protein Aggregates Experimental",
                "help_text": "Type: `file`, default: `$id.$key.protein_aggregates_experimental.csv`, example: `Protein_Aggregates_Experimental.csv`. Protein Aggregates Experimental"
            ,
                "default": "$id.$key.protein_aggregates_experimental.csv"
            }
    

}
},
    
    
    "putative cell calling settings" : {
    "title": "Putative Cell Calling Settings",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "cell_calling_data": {
                "type":
                "string",
                "description": "Type: `string`, example: `mRNA`, choices: ``mRNA`, `AbSeq`, `ATAC`, `mRNA_and_ATAC``. 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",
                "help_text": "Type: `string`, example: `mRNA`, choices: ``mRNA`, `AbSeq`, `ATAC`, `mRNA_and_ATAC``. 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",
                "enum": ["mRNA", "AbSeq", "ATAC", "mRNA_and_ATAC"]
            
            
            }
    

        ,
                "cell_calling_bioproduct_algorithm": {
                "type":
                "string",
                "description": "Type: `string`, example: `Basic`, choices: ``Basic`, `Refined``. 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",
                "help_text": "Type: `string`, example: `Basic`, choices: ``Basic`, `Refined``. 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",
                "enum": ["Basic", "Refined"]
            
            
            }
    

        ,
                "cell_calling_atac_algorithm": {
                "type":
                "string",
                "description": "Type: `string`, example: `Basic`, choices: ``Basic`, `Refined``. 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",
                "help_text": "Type: `string`, example: `Basic`, choices: ``Basic`, `Refined``. 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",
                "enum": ["Basic", "Refined"]
            
            
            }
    

        ,
                "exact_cell_count": {
                "type":
                "integer",
                "description": "Type: `integer`, example: `10000`. Set a specific number (\u003e=1) of cells as putative, based on those with the highest error-corrected read count\n",
                "help_text": "Type: `integer`, example: `10000`. Set a specific number (\u003e=1) of cells as putative, based on those with the highest error-corrected read count\n"
            
            }
    

        ,
                "expected_cell_count": {
                "type":
                "integer",
                "description": "Type: `integer`, example: `20000`. Guide the basic putative cell calling algorithm by providing an estimate of the number of cells expected",
                "help_text": "Type: `integer`, example: `20000`. 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"
            
            }
    

}
},
    
    
    "intronic reads settings" : {
    "title": "Intronic Reads Settings",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "exclude_intronic_reads": {
                "type":
                "boolean",
                "description": "Type: `boolean`, example: `false`. By default, the flag is false, and reads aligned to exons and introns are considered and represented in molecule counts",
                "help_text": "Type: `boolean`, example: `false`. 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"
            
            }
    

}
},
    
    
    "multiplex settings" : {
    "title": "Multiplex Settings",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "sample_tags_version": {
                "type":
                "string",
                "description": "Type: `string`, example: `human`, choices: ``human`, `mouse`, `flex`, `nuclei_includes_mrna`, `nuclei_atac_only``. 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",
                "help_text": "Type: `string`, example: `human`, choices: ``human`, `mouse`, `flex`, `nuclei_includes_mrna`, `nuclei_atac_only``. 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",
                "enum": ["human", "mouse", "flex", "nuclei_includes_mrna", "nuclei_atac_only"]
            
            
            }
    

        ,
                "tag_names": {
                "type":
                "string",
                "description": "Type: List of `string`, example: `4-mySample;9-myOtherSample;6-alsoThisSample`, multiple_sep: `\";\"`. Specify the tag number followed by \u0027-\u0027 and the desired sample name to appear in Sample_Tag_Metrics",
                "help_text": "Type: List of `string`, example: `4-mySample;9-myOtherSample;6-alsoThisSample`, multiple_sep: `\";\"`. Specify the tag number followed by \u0027-\u0027 and the desired sample name to appear in Sample_Tag_Metrics.csv\nDo not use the special characters: \u0026, (), [], {},  \u003c\u003e, ?, |\n"
            
            }
    

}
},
    
    
    "vdj arguments" : {
    "title": "VDJ arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "vdj_version": {
                "type":
                "string",
                "description": "Type: `string`, example: `human`, choices: ``human`, `mouse`, `humanBCR`, `humanTCR`, `mouseBCR`, `mouseTCR``. If VDJ was done, specify the appropriate option: human, mouse, humanBCR, humanTCR, mouseBCR, mouseTCR\n",
                "help_text": "Type: `string`, example: `human`, choices: ``human`, `mouse`, `humanBCR`, `humanTCR`, `mouseBCR`, `mouseTCR``. If VDJ was done, specify the appropriate option: human, mouse, humanBCR, humanTCR, mouseBCR, mouseTCR\n",
                "enum": ["human", "mouse", "humanBCR", "humanTCR", "mouseBCR", "mouseTCR"]
            
            
            }
    

}
},
    
    
    "atac options" : {
    "title": "ATAC options",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "predefined_atac_peaks": {
                "type":
                "string",
                "description": "Type: `file`, example: `predefined_peaks.bed`. An optional BED file containing pre-established chromatin accessibility peak regions for generating the ATAC cell-by-peak matrix",
                "help_text": "Type: `file`, example: `predefined_peaks.bed`. An optional BED file containing pre-established chromatin accessibility peak regions for generating the ATAC cell-by-peak matrix."
            
            }
    

}
},
    
    
    "additional options" : {
    "title": "Additional options",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "run_name": {
                "type":
                "string",
                "description": "Type: `string`, default: `sample`. Specify a run name to use as the output file base name",
                "help_text": "Type: `string`, default: `sample`. 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"
            ,
                "default": "sample"
            }
    

        ,
                "generate_bam": {
                "type":
                "boolean",
                "description": "Type: `boolean`, default: `false`. Specify whether to create the BAM file output\n",
                "help_text": "Type: `boolean`, default: `false`. Specify whether to create the BAM file output\n"
            ,
                "default": "False"
            }
    

        ,
                "long_reads": {
                "type":
                "boolean",
                "description": "Type: `boolean`. Use STARlong (default: undefined - i",
                "help_text": "Type: `boolean`. 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"
            
            }
    

}
},
    
    
    "advanced options" : {
    "title": "Advanced options",
    "type": "object",
    "description": "NOTE: Only change these if you are really sure about what you are doing\n",
    "properties": {
    
        
                "custom_star_params": {
                "type":
                "string",
                "description": "Type: `string`, example: `--alignIntronMax 6000 --outFilterScoreMinOverLread 0.1 --limitOutSJcollapsed 2000000`. Modify STAR alignment parameters - Set this parameter to fully override default STAR mapping parameters used in the pipeline",
                "help_text": "Type: `string`, example: `--alignIntronMax 6000 --outFilterScoreMinOverLread 0.1 --limitOutSJcollapsed 2000000`. 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"
            
            }
    

        ,
                "custom_bwa_mem2_params": {
                "type":
                "string",
                "description": "Type: `string`, example: `-k 16 -w 200 -r`. 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 \nDo NOT set any non-mapping related params like `-C`, `-t`, etc",
                "help_text": "Type: `string`, example: `-k 16 -w 200 -r`. 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 \nDo NOT set any non-mapping related params like `-C`, `-t`, etc.\nWe use bwa-mem2 version 2.2.1\n"
            
            }
    

}
},
    
    
    "cwl-runner arguments" : {
    "title": "CWL-runner arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "parallel": {
                "type":
                "boolean",
                "description": "Type: `boolean`, default: `true`. Run jobs in parallel",
                "help_text": "Type: `boolean`, default: `true`. Run jobs in parallel."
            ,
                "default": "True"
            }
    

        ,
                "timestamps": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Add timestamps to the errors, warnings, and notifications",
                "help_text": "Type: `boolean_true`, default: `false`. Add timestamps to the errors, warnings, and notifications."
            ,
                "default": "False"
            }
    

}
},
    
    
    "undocumented arguments" : {
    "title": "Undocumented arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "abseq_umi": {
                "type":
                "integer",
                "description": "Type: `integer`. ",
                "help_text": "Type: `integer`. "
            
            }
    

        ,
                "target_analysis": {
                "type":
                "boolean",
                "description": "Type: `boolean`. ",
                "help_text": "Type: `boolean`. "
            
            }
    

        ,
                "vdj_jgene_evalue": {
                "type":
                "number",
                "description": "Type: `double`. e-value threshold for J gene",
                "help_text": "Type: `double`. e-value threshold for J gene. The e-value threshold for J gene call by IgBlast/PyIR, default is set as 0.001\n"
            
            }
    

        ,
                "vdj_vgene_evalue": {
                "type":
                "number",
                "description": "Type: `double`. e-value threshold for V gene",
                "help_text": "Type: `double`. e-value threshold for V gene. The e-value threshold for V gene call by IgBlast/PyIR, default is set as 0.001\n"
            
            }
    

        ,
                "write_filtered_reads": {
                "type":
                "boolean",
                "description": "Type: `boolean`. ",
                "help_text": "Type: `boolean`. "
            
            }
    

}
},
    
    
    "nextflow input-output arguments" : {
    "title": "Nextflow input-output arguments",
    "type": "object",
    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
    "properties": {
    
        
                "publish_dir": {
                "type":
                "string",
                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
            
            }
    

        ,
                "param_list": {
                "type":
                "string",
                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
                "hidden": true
            
            }
    

}
}
},
"allOf": [

    {
    "$ref": "#/definitions/inputs"
    },

    {
    "$ref": "#/definitions/outputs"
    },

    {
    "$ref": "#/definitions/references"
    },

    {
    "$ref": "#/definitions/multiplex outputs"
    },

    {
    "$ref": "#/definitions/vdj outputs"
    },

    {
    "$ref": "#/definitions/atac-seq outputs"
    },

    {
    "$ref": "#/definitions/abseq cell calling outputs"
    },

    {
    "$ref": "#/definitions/putative cell calling settings"
    },

    {
    "$ref": "#/definitions/intronic reads settings"
    },

    {
    "$ref": "#/definitions/multiplex settings"
    },

    {
    "$ref": "#/definitions/vdj arguments"
    },

    {
    "$ref": "#/definitions/atac options"
    },

    {
    "$ref": "#/definitions/additional options"
    },

    {
    "$ref": "#/definitions/advanced options"
    },

    {
    "$ref": "#/definitions/cwl-runner arguments"
    },

    {
    "$ref": "#/definitions/undocumented arguments"
    },

    {
    "$ref": "#/definitions/nextflow input-output arguments"
    }
]
}
