{{ run_name }} Pipeline Results Summary

Bioproducts
{{section}}
{{section}}
ATAC
{{section|replace("ATAC", "")}}
{{section|replace("ATAC", "")}}
{{section}}

{{num_metric_alerts}}
{{section}}

{% for section in sections -%} {% if section == 'Summary' %}

Summary

Putative Cells: {{ putative_cells }}

{% if hasMRNA == 1 or hasAbSeq == 1 or cell_calling_data == 'VDJ' %}

{% if hasATAC == 1 %}

Bioproducts

{% endif %}

{% for row in summary_headers1 %} {% endfor %} {% for list in summary_values1 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %}

{{ summary_headers1[loop.index0] }}
{{ val }}

{% for row in summary_headers2 %} {% endfor %} {% for list in summary_values2 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %}

{{ summary_headers2[loop.index0] }}
{{ val }}

{% endif %} {% if (hasMRNA == 1 or hasAbSeq == 1 or cell_calling_data == 'VDJ') and hasATAC == 1 %}

{% endif %} {% if hasATAC == 1 %}

ATAC

{% for row in atac_summary_headers1 %} {% endfor %} {% for list in atac_summary_values1 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %}

{{ atac_summary_headers1[loop.index0] }}
{{ val }}

{% for row in atac_summary_headers2 %} {% endfor %} {% for list in atac_summary_values2 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %}

{{ atac_summary_headers2[loop.index0] }}
{{ val }}

{% endif %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'Graphs' and cell_calling_data != 'VDJ' %}

Graphs

{% if hasTsneCoords == 1 or hasUmapCoords == 1 %}

{% if hasTsneCoords == 1 and hasUmapCoords == 1 %} tSNE UMAP {% endif %}

{% else %}

No graphs available. (Usually due to too few or too many cells)

{% endif %}

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{% if hasTsneCoords == 1 or hasUmapCoords == 1 %}

Select Gene or AbSeq: A small selection of the most highly, widely, and variably expressed genes plus all AbSeq targets are listed. The AbSeq targets and mRNA genes are sorted by total expression (highest to lowest) separately. The bioproduct with the highest expression is selected by default. To view all data, load the dataset in the BD Cellismo data visualization tool

{% for gene in histo_genes %} {% if gene != 'Cell_Index' %} {% endif %} {% endfor %}

{% endif %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'Read Flow Diagram' %}

Read Flow Diagram

Select Library:

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'Sequencing Quality' %}

Bioproduct Sequencing Quality

{% for row in sequence_quality_headers %} {% endfor %} {% for list in sequence_quality_values %} {% set rowloop = loop %} {% for val in list %} {% endfor %}

{{ sequence_quality_headers[loop.index0] }}
{{ val }} {% endfor %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'Library Quality' %}

Bioproduct Library Quality

{% for row in library_quality_headers %} {% endfor %} {% for list in library_quality_values %} {% set rowloop = loop %} {% for val in list %} {% endfor %}

{{ library_quality_headers[loop.index0] }}
{{ val }} {% endfor %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'Alignment Categories' %}

Bioproduct Alignment Categories

{% for row in alignment_headers %} {% endfor %} {% for list in alignment_values %} {% set rowloop = loop %} {% for val in list %} {% endfor %}

{{ alignment_headers[loop.index0] }}
{{ val }} {% endfor %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'Reads and Molecules' and cell_calling_data != 'VDJ' %}

Bioproduct Reads and Molecules

{% for row in r_and_m_headers %} {% endfor %} {% for list in r_and_m_values %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %}

{{r_and_m_headers[loop.index0] }}
{{ val }}

Sequencing Saturation Plot(s):

Click for more info

{% for biop_type, data in seq_saturation_plot_data['Seq_Saturation'].items() %}

{% endfor %}

{% if seq_saturation_plot_data['Seq_Saturation'].values() | selectattr('K') | list %}

Sequencing Depth for Target Saturation:

{% for biop_type, data in seq_saturation_plot_data['Seq_Saturation'].items() %} {% if data.K %}

Target Sequencing Saturation: % {% if data.perc_raw_reads < 99 %} {{ biop_type }} reads in input FASTQs: % {% endif %}

{% endif %} {% endfor %}

{% endif %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'ATAC Sequencing Quality' %}

ATAC Sequencing Quality

{% for row in atac_sequence_quality_headers %} {% endfor %} {% for list in atac_sequence_quality_values %} {% set rowloop = loop %} {% for val in list %} {% endfor %}

{{ atac_sequence_quality_headers[loop.index0] }}
{{ val }} {% endfor %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'ATAC Library Quality' %}

ATAC Library Quality

{% for row in atac_library_quality_headers %} {% endfor %} {% for list in atac_library_quality_values %} {% set rowloop = loop %} {% for val in list %} {% endfor %}

{{ atac_library_quality_headers[loop.index0] }}
{{ val }} {% endfor %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'ATAC Alignment Categories' %}

ATAC Alignment Categories

{% for row in atac_alignment_headers %} {% endfor %} {% for list in atac_alignment_values %} {% set rowloop = loop %} {% for val in list %} {% endfor %}

{{ atac_alignment_headers[loop.index0] }}
{{ val }} {% endfor %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'ATAC Fragments' %}

ATAC Fragments

{% for row in atac_fragment_headers %} {% endfor %} {% for list in atac_fragment_values %} {% set rowloop = loop %} {% for val in list %} {% endfor %}

{{ atac_fragment_headers[loop.index0] }}
{{ val }} {% endfor %}

{% if atac_frag_dist_plot_dataurl %}

{% endif %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'ATAC Peaks' %}

ATAC Peaks

{% for row in atac_peak_headers %} {% endfor %} {% for list in atac_peak_values %} {% set rowloop = loop %} {% for val in list %} {% endfor %}

{{ atac_peak_headers[loop.index0] }}
{{ val }} {% endfor %}

{% if atac_tss_plot_dataurl %}

{% endif %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'Cells' %}

Cells

{% for row in cell_summary_headers1 %} {% if not loop.first %}
{% endif %}

{{cell_summary_values1[loop.index0]}} {% if loop.first %}
{% endif %} {% endfor %}

{% if hasJointCells == 1 %}

{% for row in cell_summary_headers2 %} {% if not loop.first %}
{% endif %}

{{cell_summary_values2[loop.index0]}} {% if loop.first %}
{% endif %} {% endfor %}

{% for row in cell_summary_headers3 %} {% if not loop.first %}
{% endif %}

{{cell_summary_values3[loop.index0]}} {% if loop.first %}
{% endif %} {% endfor %}

{% endif %}

{% if hasCells or hasATACCells or hasATACScatterCells or hasJointCells or hasTCRCells or hasBCRCells or hasVDJCells %}

{% set dropdown_needed = ( (hasATACCells and hasATACScatterCells) or hasJointCells or (hasTCRCells and hasBCRCells) ) %} {% if dropdown_needed %}

{% endif %}

{% if hasMRNA == 1 or hasAbSeq == 1 %} {% if hasATAC == 1 %}

Bioproduct Cells

{% endif %}

{% for row in cell_headers %} {% endfor %} {% for list in cell_values %} {% set rowloop = loop %} {% for val in list %} {% endfor %}

{{cell_headers[loop.index0] }}
{{ val }} {% endfor %}

{% if hasMRNA %}

Median Bioproducts per Cell Plot:

Click for more info

{% for biop_type, data in seq_saturation_plot_data['Median_Bioproducts_per_Cell'].items() %} {% if biop_type == 'mRNA' %}

{% endif %} {% endfor %}

{% endif %}

{% endif %} {% if hasATAC == 1 %}

ATAC Cells

{% for row in atac_cell_headers %} {% endfor %} {% for list in atac_cell_values %} {% set rowloop = loop %} {% for val in list %} {% endfor %}

{{atac_cell_headers[loop.index0] }}
{{ val }} {% endfor %}

{% endif %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'Sample Multiplexing' %}

Sample Multiplexing

Valid Reads aligned to Sample Tags

Pct Reads from Putative Cells

{% for row in sample_multiplexing_headers1 %} {% endfor %} {% for list in sample_multiplexing_values1 %} {% set rowloop = loop %} {% for val in list %} {% endfor %}

{{sample_multiplexing_headers1[loop.index0] }}
{{ val }} {% endfor %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'VDJ' %}

VDJ

{{vdj_name1}} {% for row in vdj_headers1 %} {% endfor %} {% if hasBCRdata == 1 %} {% for list in vdj_bcr1 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %} {% for list in vdj_sub_values1_1 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %} {% endif %} {% if hasTCRdata == 1 %} {% for list in vdj_tcr1 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %} {% for list in vdj_sub_values1_2 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %} {% endif %}

	{{ vdj_headers1[loop.index0] }}
	{{ val }}
	{{ val }}
	{{ val }}
	{{ val }}

{{vdj_name2}} {% for row in vdj_headers2 %} {% endfor %} {% if hasBCRdata == 1 %} {% for list in vdj_bcr2 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %} {% for list in vdj_sub_values2_1 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %} {% endif %} {% if hasTCRdata == 1 %} {% for list in vdj_tcr2 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %} {% for list in vdj_sub_values2_2 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %} {% endif %}

	{{ vdj_headers2[loop.index0] }}
	{{ val }}
	{{ val }}
	{{ val }}
	{{ val }}

{% if cell_basic_num_cell > 0 or tcr_cell_basic_num_cell > 0 or bcr_cell_basic_num_cell > 0 or vdj_cell_basic_num_cell > 0 %} Cell Type VDJ Metrics: {% for row in vdj_headers3 %} {% endfor %} {% for list in vdj_values3 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %}

{{ vdj_headers3[loop.index0] }}
{{ val }}

{% for row in vdj_headers4 %} {% endfor %} {% for list in vdj_values4 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %}

{{ vdj_headers4[loop.index0] }}
{{ val }}

{% for row in vdj_headers5 %} {% endfor %} {% for list in vdj_values5 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %}

{{ vdj_headers5[loop.index0] }}
{{ val }}

{% for row in vdj_headers6 %} {% endfor %} {% for list in vdj_values6 %} {% set rowloop = loop %} {% for val in list %} {% endfor %} {% endfor %}

{{ vdj_headers6[loop.index0] }}
{{ val }}

{% endif %}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'Pipeline Inputs' %}

Pipeline Inputs

Pipeline version: {{pipeline_version}}

Pipeline Start Time: {{start_time}}

AbSeq Reference:

{{ abseq_ref[loop.index0] }}

Reference Files Archive:

{{ref_archive}}

Supplemental Reference:

{{ supp_ref[loop.index0] }}

Targeted Reference:

{{ targ_ref[loop.index0] }}

ATAC Predefined Peak Regions:

{{predef_atac_peaks}}

Reads:

{{ reads[loop.index0] }}

ATAC Reads:

{{ reads_atac[loop.index0] }}

Multiplexing Settings

Sample Tags Version: {{tag_version}}
Tag Names: {{tag_names}}

VDJ Settings

VDJ Species Version: {{vdj_species_version}}

Putative Cell Calling Settings

Cell Calling Data: {{cell_calling_data}}
Cell Calling Bioproduct Algorithm: {{cell_calling_bioproduct_alg}}
Cell Calling ATAC Algorithm: {{cell_calling_atac_alg}}
Exact Cell Count: {{exact_count}}
Expected Cell Count: {{expected_count}}

Exclude Intronic reads: {{exclude_intronic_reads}}

Generate Bam output: {{generate_bam}}

{% endif %} {% endfor %} {% for section in sections -%} {% if section == 'Metric Alerts' %}

Metric Alerts

(Under development)

{% if metric_alerts %} {% for list in metric_alerts %}

{{val}}

{% endfor %}

{% else %}

No alerts detected

{% endif %}

{% endif %} {% endfor %}

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Pipeline Version: {{pipeline_version}}

{{start_time}}

Summary

Bioproducts

ATAC

Graphs

Read Flow Diagram

Select Library:

Bioproduct Sequencing Quality

Bioproduct Library Quality

Bioproduct Alignment Categories

Bioproduct Reads and Molecules

ATAC Sequencing Quality

ATAC Library Quality

ATAC Alignment Categories

ATAC Fragments

ATAC Peaks

Cells

Bioproduct Cells

ATAC Cells

Sample Multiplexing

VDJ

Pipeline Inputs

Metric Alerts

(Under development)