yascp

nf-core/yascp: Output

Introduction

This documentation provides a comprehensive overview of the outputs generated by the pipeline.

The pipeline will create the following files in your working directory:

work            # Nextflow working directory
results         # Final results (configurable, see below)
.nextflow_log   # Log file from Nextflow
# Other Nextflow hidden files, eg. history of pipeline runs and old logs.

The structure of the results folder is outlined below, providing a snapshot of the diverse outputs from various stages of the pipeline:

• preprocessing: Contains data split by modality and preprocessing outputs
• doublet_detection: Includes results identifying artificial doublet cells.
• deconvolution: Contains outputs from disentangling mixtures of cells from different donors.
• celltype_assignemt: Houses results of cell classification into specific types.
• clustering_and_integration: Contains clustered cells grouped by similarities and integrated datasets.
• citeseq: Includes CITE-seq data, linking transcriptomic and proteomic profiles.
• handover: Contains the final processed results.
• pipeline_info: Stores metadata and logs detailing the pipeline execution process.
• yascp_inputs:

Detailed explanations of each output folder and their corresponding steps are provided below:

preprocessing

The preprocessing folder contains the following subdirectories:

• data_modalities_split
  This folder contains raw and filtered quantification data separated by modality (CITE-seq or hashtag).

• resources
  This folder contains genotype assembly and input files for the test dataset.

• subset_genotypes
  This folder is created only if VCF IDs are specified in the input TSV file. It contains genotypes divided from the pools.

Click to view detailed folder structure

``` preprocessing/ ├── data_modalities_split │   ├── filterd │   │   └── Pool1 │   │   ├── Gene_Expression-Pool1.h5ad │   │   └── Pool1__Gene_Expression │   └── raw │   └── Pool1 │   ├── Gene_Expression-Pool1.h5ad │   └── Pool1__Gene_Expression ├── recourses │   ├── Done.tmp │   ├── full_test_dataset │   ├── input_test_data_file.tsv │   └── input_test_vcf_file.tsv └── subset_genotypes ├── Genotype___AllExpectedGT_Pool1 └── Genotypes_all_pools.tsv ```

doublet_detection

The doublet_detection folder contains the following subdirectories:

• DoubletFinder, DoubletDecon, scDblFinder, SCDS
  Each folder contains TSV files for each pool. These files include barcodes and labels indicating whether each cell is a singlet or a doublet.

• scrublet
  This folder contains TSV files for each pool with barcodes and labels indicating whether each cell is a multiplet or not. Additionally, this folder includes a subdirectory with plots.

• doublet_results_combined
  This folder contains TSV files for each pool with barcodes and combined labels from multiple tools: Scrublet, SCDS, scDblFinder, DoubletDecon, and DoubletFinder.

• droplet_type_distribution
  This folder contains PNG files with graphs visualizing the distribution of droplet types.

Click to view detailed folder structure

``` doublet_detection ├── DoubletDecon │   └── Pool1__DoubletDecon_doublets_singlets.tsv ├── DoubletFinder │   └── Pool1__DoubletFinder_doublets_singlets.tsv ├── doublet_results_combined │   └── Pool1__doublet_results_combined.tsv ├── droplet_type_distribution │   └── Pool1__droplet_type_distribution.png ├── scDblFinder │   └── Pool1__scDblFinder_doublets_singlets.tsv ├── SCDS │   └── Pool1__scds_doublets_singlets.tsv └── scrublet ├── plots │   ├── Pool1boxplot_total_umi_counts.png │   ├── Pool1histogram_multiplet_scores_log.png │   ├── Pool1histogram_multiplet_scores.png │   └── Pool1histogram_multiplet_zscores.png └── Pool1scrublet.tsv ```

deconvolution

The deconvolution folder contains the following subdirectories:

• vireo_raw
  This folder contains genotypes if run in genotype-aware mode
  Click to view detailed folder structure

  ``` vireo_raw ├── correlations.png ├── Pool1 │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz.csi │   ├── sub_Pool1_Expected.vcf.gz │   └── vireo_Pool1 ├── donor_corelations_matrix.tsv └── matched_donors.txt ```
• vireo_processed
  The vireo_processed folder contains genotypes renamed to imitate genotype absent mode to ensure consistency in the downstream pipeline tasks
  Click to view detailed folder structure

  ``` vireo_processed ├── assignments_all_pools.tsv └── Pool1 ├── GT_replace_donor_ids_false.tsv ├── GT_replace_GT_donors.vireo_false.vcf.gz ├── GT_replace_Pool1_assignments_false.tsv ├── GT_replace_Pool1__exp.sample_summary_false.txt └── GT_replace_Pool1.sample_summary_false.txt ```
• vireo_sub
  The vireo_sub folder contains vireo permutations to ensure stability in cell assignment
  Click to view detailed folder structure

  ``` vireo_sub └── Pool1    ├── vireo_____1    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz.csi    │   ├── sub_Pool1_Expected.vcf.gz    │   └── vireo_Pool1___1    ├── vireo_____10    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz.csi    │   ├── sub_Pool1_Expected.vcf.gz    │   └── vireo_Pool1___10    ├── vireo_____2    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz.csi    │   ├── sub_Pool1_Expected.vcf.gz    │   └── vireo_Pool1___2    ├── vireo_____3    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz.csi    │   ├── sub_Pool1_Expected.vcf.gz    │   └── vireo_Pool1___3    ├── vireo_____4    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz.csi    │   ├── sub_Pool1_Expected.vcf.gz    │   └── vireo_Pool1___4    ├── vireo_____5    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz.csi    │   ├── sub_Pool1_Expected.vcf.gz    │   └── vireo_Pool1___5    ├── vireo_____6    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz.csi    │   ├── sub_Pool1_Expected.vcf.gz    │   └── vireo_Pool1___6    ├── vireo_____7    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz.csi    │   ├── sub_Pool1_Expected.vcf.gz    │   └── vireo_Pool1___7    ├── vireo_____8    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz    │   ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz.csi    │   ├── sub_Pool1_Expected.vcf.gz    │   └── vireo_Pool1___8    └── vireo_____9    ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz    ├── dubs_removed__Study_Merge_AllExpectedGT_QW4IKXM1N_out.vcf.gz.csi    ├── sub_Pool1_Expected.vcf.gz    └── vireo_Pool1___9 ```
• infered_genotypes
  The infered_genotypes folder contains genotypes called from single-cell data (per donor in a pool)
  Click to view detailed folder structure

  ``` infered_genotypes └── Pool1    ├── Pool1_headfix_vireo.vcf.gz    └── Pool1_headfix_vireo.vcf.gz.tbi ```
• split_donor_h5ad
  The split_donor_h5ad folder contains per donor quantification matrix and additional metadata
  Click to view detailed folder structure

  ``` split_donor_h5ad └── Pool1 ├── cell_belongings.tsv ├── donor_level_anndata │   ├── donor0.Pool1.barcodes.tsv │   ├── donor0.Pool1.h5ad │   ├── donor1.Pool1.barcodes.tsv │   ├── donor1.Pool1.h5ad │   ├── donor2.Pool1.barcodes.tsv │   ├── donor2.Pool1.h5ad │   ├── doublet.Pool1.barcodes.tsv │   ├── doublet.Pool1.h5ad │   ├── unassigned.Pool1.barcodes.tsv │   └── unassigned.Pool1.h5ad ├── Pool1.donors.h5ad.assigned.tsv ├── Pool1__donors.h5ad.assigned.tsv ├── Pool1.donors.h5ad.tsv ├── Pool1__donors.h5ad.tsv ├── Pool1_exp__donor_n_cells.tsv ├── Pool1.h5ad.tsv ├── vireo_annot.Pool1.h5ad └── Vireo_plots.pdf ```
• cellsnp
  The cellsnp folder contains genotypes called from single-cell data per droplet/cell
  Click to view detailed folder structure

  ``` cellsnp └── cellsnp_Pool1 ├── cellSNP.base.vcf.gz ├── cellSNP.cells.vcf.gz ├── cellSNP.samples.tsv ├── cellSNP.tag.AD.mtx ├── cellSNP.tag.DP.mtx └── cellSNP.tag.OTH.mtx ```
• concordances
  The concordances contains statistics describing how confident the cell-inferred genotype aligns with the reference genotypes.
  Click to view detailed folder structure

  ``` concordances ├── all_variants_description.tsv ├── becoming_different_donor.png ├── becoming_doublet_donor.png ├── becoming_unassigned_donor.png ├── Pool1 │   ├── 1090095_1090095-donor3--each_cells_comparison_with_other_donor.tsv │   ├── 1709635_1709635-donor5--each_cells_comparison_with_other_donor.tsv │   ├── 2288590_2288590-donor6--each_cells_comparison_with_other_donor.tsv │   ├── 2743244_2743244-donor7--each_cells_comparison_with_other_donor.tsv │   ├── 2768849_2768849-donor4--each_cells_comparison_with_other_donor.tsv │   ├── 2998395_2998395-donor2--each_cells_comparison_with_other_donor.tsv │   ├── 3183427_3183427-donor0--each_cells_comparison_with_other_donor.tsv │   ├── 3699286_3699286-donor1--each_cells_comparison_with_other_donor.tsv │   ├── 4853673_4853673-donor9--each_cells_comparison_with_other_donor.tsv │   ├── 5154993_5154993-donor8--each_cells_comparison_with_other_donor.tsv │   ├── becoming_different_donor.png │   ├── becoming_doublet_donor.png │   ├── becoming_unassigned_donor.png │   ├── cell_belongings.tsv │   ├── cellSNP.cells.vcf.gz │   ├── Pool1__joined_df_for_plots.tsv │   ├── Pool1_subsampling_donor_swap_quantification.tsv │   ├── Discordant_reads_becoming_different_donor_no0.png │   ├── Discordant_reads_becoming_different_donor.png │   ├── Discordant_reads_by_n_sites_becoming_different_donor_no0.png │   ├── Discordant_reads_by_n_sites_becoming_different_donor.png │   ├── discordant_sites_in_other_donors_noA2G.tsv │   ├── Nr_discordant_uninformative_becoming_different_donor.png │   ├── sites_becoming_different_donor_no0.png │   ├── sites_becoming_different_donor.png │   ├── sites_becoming_different_donor_probs.png │   ├── sites_becoming_doublet_donor.png │   ├── sites_becoming_unassigned_donor.png │   ├── sites_vs_concordance.png │   ├── stats_Pool1_gt_donor_assignments.csv │   ├── sub_Pool1_Expected.vcf.gz │   ├── sub_Pool1_GT_Matched.vcf.gz │   ├── subplot_sites_vs_concordance.png │   └── Total_reads_becoming_different_donor.png ├── Discordant_reads_becoming_different_donor_no0.png ├── Discordant_reads_becoming_different_donor.png ├── Discordant_reads_by_n_sites_becoming_different_donor_no0.png ├── Discordant_reads_by_n_sites_becoming_different_donor.png ├── joined_df_for_plots.tsv ├── Nr_discordant_uninformative_becoming_different_donor.png ├── sites_becoming_different_donor_no0.png ├── sites_becoming_different_donor.png ├── sites_becoming_different_donor_probs.png ├── sites_becoming_doublet_donor.png ├── sites_becoming_unassigned_donor.png ├── sites_vs_concordance.png ├── subplot_sites_vs_concordance.png └── Total_reads_becoming_different_donor.png ```
• gtmatch
  If genotypes are provided it contains the results of donors assigned by gtcheck.
  Click to view detailed folder structure

  ``` gtmatch/ ├── assignments_all_pools.tsv └── Pool1 ├── Done.tmp ├── Expected_Withing_expected_Pool1.genome ├── GT_replace_PiHAT_Stats_File_Pool1.csv ├── InferedExpected_Expected_Infered_Pool1.genome ├── InferedGTMatched_Expected_Infered_Pool1.genome ├── InferedOnly_Withing_pool_Pool1.genome ├── PiHAT_Stats_File_Pool1.csv ├── Pool1_gt_donor_assignments.csv ├── pool_Pool1_panel_Pool1_Onek1K_gtcheck_donor_assignments.csv ├── pool_Pool1_panel_Pool1_Onek1K_gtcheck_score_table.csv └── stats_Pool1_gt_donor_assignments.csv ```

celltype_assignemt

The celltype_assignemt folder contains the following subdirectories and files:

• All_Celltype_Assignments.tsv
  A combined file with results per barcode/droplet/cell.

• donor_celltype_report.tsv
  Summarized cell counts per donor.

• tranche_celltype_report.tsv
  Summarized cell counts per tranche.

• scpred
  This folder contains the results of scPred

• azimuth
  This folder contains the results of azimuth

• celltypist
  This folder contains the results of celltypist

Click to view detailed folder structure

``` celltype_assignemt/ ├── All_Celltype_Assignments.tsv ├── azimuth │   └── PBMC │   ├── AZ_1.pre_QC_adata_Pool1_Pool1_celltype.l1.mapping_score_umap.pdf │   ├── AZ_1.pre_QC_adata_Pool1_Pool1_celltype.l1.mapping_score_vln.pdf │   ├── AZ_1.pre_QC_adata_Pool1_Pool1_celltype.l1.ncells_by_type_barplot.pdf │   ├── AZ_1.pre_QC_adata_Pool1_Pool1_celltype.l1.prediction_score_umap.pdf │   ├── AZ_1.pre_QC_adata_Pool1_Pool1_celltype.l1.prediction_score_vln.pdf │   ├── AZ_1.pre_QC_adata_Pool1_Pool1_celltype.l1.query_umap.pdf │   └── AZ_1.pre_QC_adata_Pool1_Pool1_predicted_celltype_l1.tsv ├── celltypist │   ├── COVID19_Immune_Landscape │   │   └── Pool1 │   │   ├── Pool1___COVID19_Immune_Landscape___decision_matrix.csv │   │   ├── Pool1___COVID19_Immune_Landscape___predicted_labels.csv │   │   ├── Pool1___COVID19_Immune_Landscape___probability_matrix.csv │   │   ├── Pool1_majority_voting.pdf │   │   ├── Pool1_over_clustering.pdf │   │   └── Pool1_predicted_labels.pdf │   ├── Immune_All_High │   │   └── Pool1 │   │   ├── Pool1___Immune_All_High___decision_matrix.csv │   │   ├── Pool1___Immune_All_High___predicted_labels.csv │   │   ├── Pool1___Immune_All_High___probability_matrix.csv │   │   ├── Pool1_majority_voting.pdf │   │   ├── Pool1_over_clustering.pdf │   │   └── Pool1_predicted_labels.pdf │   └── Immune_All_Low │   └── Pool1 │   ├── Pool1___Immune_All_Low___decision_matrix.csv │   ├── Pool1___Immune_All_Low___predicted_labels.csv │   ├── Pool1___Immune_All_Low___probability_matrix.csv │   ├── Pool1_majority_voting.pdf │   ├── Pool1_over_clustering.pdf │   └── Pool1_predicted_labels.pdf ├── donor_celltype_report.tsv ├── scpred │   ├── AZ_1.pre_QC_adata_Pool1_AZ_1.pre_QC_adata_Pool1__scpred_prediction.tsv │   └── AZ_1.pre_QC_adata_Pool1_hier_scpred.RDS └── tranche_celltype_report.tsv ```

clustering_and_integration

The clustering_and_integration folder contains integrated and clustered data, along with statistics and plots that describe the performance of the integration and clustering processes.

Click to view detailed folder structure

``` clustering_and_integration/ ├── normalize=total_count.vars_to_regress=none │   ├── adatametadata.tsv.gz │   ├── adatanormalized.h5ad │   ├── adatanormalized_pcacounts.h5ad │   ├── adatanormalized_pca.h5ad │   ├── adatanormalized_pcaknee.tsv │   ├── adatapcs.tsv.gz │   ├── donor_level_anndata_QCfiltered │   │   └── Pool1___sample_QCd_adata.h5ad │   ├── plots │   ├── reduced_dims-null-bbknn.batch=experiment_id.n_pcs=20 │   │   ├── cluster.number_neighbors=-1.method=leiden.resolution=0.1 │   │   │   ├── clustering_0.1clustered.h5ad │   │   │   ├── clustering_0.1clustered.tsv.gz │   │   │   ├── dotplot_sampleclustering_0.1clustered_ncells0.pdf │   │   │   ├── dotplot_sampleclustering_0.1clustered_ncellsless5.pdf │   │   │   ├── dotplot_sampleclustering_0.1clustered.pdf │   │   │   ├── plots │   │   │   ├── sccaf │   │   │   └── validate_resolution │   │   ├── cluster.number_neighbors=-1.method=leiden.resolution=0.5 │   │   ├── cluster.number_neighbors=-1.method=leiden.resolution=1.0 │   │   ├── cluster.number_neighbors=-1.method=leiden.resolution=5.0 │   │   ├── outfile_adatabbknn.h5ad │   │   ├── plots │   │   ├── reduced_dims.tsv.gz │   │   ├── resolution_tuningmerged_model_report.tsv.gz │   │   ├── resolution_tuningmerged_test_result.tsv.gz │   │   └── umap_gather_out.h5ad │   ├── reduced_dims-null-harmony.n_pcs=20.variables=experiment_id.thetas=1.0 │   │   ├── cluster.number_neighbors=15.method=leiden.resolution=0.1 │   │   ├── cluster.number_neighbors=15.method=leiden.resolution=0.5 │   │   ├── cluster.number_neighbors=15.method=leiden.resolution=1.0 │   │   ├── cluster.number_neighbors=15.method=leiden.resolution=5.0 │   │   ├── plots │   │   ├── reduced_dims.tsv.gz │   │   ├── resolution_tuningmerged_model_report.tsv.gz │   │   ├── resolution_tuningmerged_test_result.tsv.gz │   │   └── umap_gather_out.h5ad │   └── reduced_dims-null-pca.n_pcs=20 │   ├── clustering_and_integration │   │   └── plots │   └── reduced_dims.tsv.gz └── plots ```

citeseq

The citeseq folder contains the following subdirectories:

• [DSB]
  DSB has folders for each pool which contain DSB background and removed protein counts if citeseq is in the quantification matrix

Click to view detailed folder structure

``` citeseq/ └── DSB └── Pool1 └── CITE__Pool1 ```

handover

The handover folder contains the following subdirectories:

• Summary_plots This folder contains various plots across the pipeline

• Donor_Quantification This folder contains h5ad and TSV files for each donor

• Donor_Quantification_summary This folder contains TSV files summarising information and statistics about donors and pools

• merged_h5ad This folder contains merged h5ad files from various stages of the pipeline

Click to view detailed folder structure

``` handover/ ├── Donor_Quantification ├── Donor_Quantification_summary ├── merged_h5ad └── Summary_plots ```

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