Input Data Formats

Depending on the type of data you run the pipeline with, one or more appropriate profiles should be set when running nextflow config. These profiles are indicated in the sections below.

Specifying multiple samples

All the input data parameters are compatible with the following features:

• Glob patterns

"data/10x/1k_pbmc/1k_pbmc_*/outs/"

• Comma separated paths (paths can contain glob patterns)

"data/10x/1k_pbmc/1k_pbmc_v2_chemistry/outs/, data/10x/1k_pbmc/1k_pbmc_v3_chemistry/outs/"

• Array of paths (paths can contain glob patterns)

[
    "data/10x/1k_pbmc/1k_pbmc_v2_chemistry/outs/",
    "data/10x/1k_pbmc/1k_pbmc_v3_chemistry/outs/"
]

---

Cell Ranger (10x Genomics)

Data from a standard Cell Ranger output directory can be easily ingested into the pipeline by using the proper input channel (tenx_mex or tenx_h5, depending on which file should be used). Multiple samples can be selected by providing the path to this directory using glob patterns.

/home/data/
└── cellranger
    ├── sample_A
    │   └── outs
    │       ├── filtered_feature_bc_matrix
    │       │   ├── barcodes.tsv
    │       │   ├── genes.tsv
    │       │   └── matrix.mtx
    │       └── filtered_feature_bc_matrix.h5
    └── sample_B
        └── outs
            ├── filtered_feature_bc_matrix
            │   ├── barcodes.tsv
            │   ├── genes.tsv
            │   └── matrix.mtx
            └── filtered_feature_bc_matrix.h5

MEX

To use the Cell Ranger Market Exchange (MEX) files, use the following profile when generating the config file:

-profile tenx

This profile adds the following parameter (params.data.tenx.cellranger_mex) into the generated .config file:

[...]
data {
    tenx {
        cellranger_mex = "/home/data/cellranger/sample*/outs/"
    }
}
[...]

H5

To use the Cell Ranger h5 file as input, use the following profile:

-profile tenx_h5

This profile adds the params.data.tenx.cellranger_h5 parameter into the generated .config file:

[...]
data {
    tenx {
        cellranger_h5 = "/home/data/cellranger/sample*/outs/"
    }
}
[...]

Input file detection

Setting the input directory appropriately, using a glob in the directory path in place of the sample names, will collect all the samples listed in the filtered_[feature|gene]_bc_matrix directories listed above. For example, in params.data.tenx, setting:

cellranger_mex = "/home/data/cellranger/sample*/outs/"

or

cellranger_h5 = "/home/data/cellranger/sample*/outs/"

will recursively find all 10x samples in that directory.

The pipeline will use either the outs/filtered_feature_bc_matrix/ or the outs/raw_feature_bc_matrix/ depending on the setting of the params.utils.file_converter.useFilteredMatrix (true uses filtered; false uses raw).

---

H5AD (Scanpy)

Use the following profile when generating the config file:

-profile h5ad

In the generated .config file, make sure the file_paths parameter is set with the paths to the .h5ad files:

[...]
data {
    h5ad {
        file_paths = "data/1k_pbmc_v*_chemistry_SUFFIX.SC__FILE_CONVERTER.h5ad"
        suffix = "_SUFFIX.SC__FILE_CONVERTER.h5ad"
    }
}
[...]

• The suffix parameter is used to infer the sample name from the file paths (it is removed from the input file path to derive a sample name).

In case there are multiple .h5ad files that need to be processed with different suffixes, the multi-labelled strategy should be used to define the h5ad parameter:

[...]
data {
    h5ad {
        GROUP1 {
            file_paths = "[path-to-group1-files]/*.SUFFIX1.h5ad"
            suffix = ".SUFFIX1.h5ad"
            group = ["technology", "10x"]
        }
        GROUP2 {
            file_paths = "[path-to-group1-files]/*.SUFFIX2.h5ad"
            suffix = ".SUFFIX2.h5ad"
            group = ["technology", "smart-seq2"]
        }
    }
}
[...]

Notes:

• GROUP1, GROUP2 are just example names here. They can be replaced by any value as long as they are alphanumeric (underscores are allowed).
• All the different suffix defined should unique.
• file_paths and suffix do allow list of paths/globs in the multi-labelled strategy.
• group [optional] should be an array of 2 elements where first element define the group name and the second the group value. This will add cell-based annotation for each group of files

---

Loom

Use the following profile when generating the config file:

-profile loom

In the generated .config file, make sure the file_paths parameter is set with the paths to the .loom files:

[...]
data {
    loom {
        file_paths = "data/1k_pbmc_v*_chemistry_SUFFIX.SC__FILE_CONVERTER.loom"
        suffix = "_SUFFIX.SC__FILE_CONVERTER.loom"
    }
}
[...]

• The suffix parameter is used to infer the sample name from the file paths (it is removed from the input file path to derive a sample name).

---

Seurat Rds

Use the following profile when generating the config file:

-profile seurat_rds

In the generated .config file, make sure the file_paths parameter is set with the paths to the .Rds files:

[...]
data {
    seurat_rds {
        file_paths = "data/1k_pbmc_v*_chemistry_SUFFIX.SC__FILE_CONVERTER.Rds"
        suffix = "_SUFFIX.SC__FILE_CONVERTER.Rds"
    }
}
[...]

• The pipelines expect a Seurat v3 object contained in the .Rds file. (Seurat v2 objects are currently not supported).
• The suffix parameter is used to infer the sample name from the file paths (it is removed from the input file path to derive a sample name).

---

TSV

Use the following profile when generating the config file:

-profile tsv

In the generated .config file, make sure the file_paths parameter is set with the paths to the .tsv files:

[...]
data {
    h5ad {
        file_paths = "data/1k_pbmc_v*_chemistry_SUFFIX.SC__FILE_CONVERTER.tsv"
        suffix = "_SUFFIX.SC__FILE_CONVERTER.tsv"
    }
}
[...]

• The suffix parameter is used to infer the sample name from the file paths (it is removed from the input file path to derive a sample name).

---

CSV

Use the following profile when generating the config file:

-profile csv

In the generated .config file, make sure the file_paths parameter is set with the paths to the .csv files:

[...]
data {
    h5ad {
        file_paths = "data/1k_pbmc_v*_chemistry_SUFFIX.SC__FILE_CONVERTER.csv"
        suffix = "_SUFFIX.SC__FILE_CONVERTER.csv"
    }
}
[...]

• The suffix parameter is used to infer the sample name from the file paths (it is removed from the input file path to derive a sample name).