CCBR/SINCLAIR pipeline parameters¶
SINgle CelL AnalysIs Resource
Input/output options¶
Define where the pipeline should find input data and save output data.
| Parameter | Description | Type | Default | Required | Hidden |
|---|---|---|---|---|---|
input | Path to CSV file containing information about the samples in the experiment. HelpYou will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 5 columns, and a header row. | string | assets/input_manifest.csv | True | |
contrast | Path to CSV file with contrast specification | string | assets/contrast_manifest.csv | True | |
outdir | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | string | output | True | |
run_cellranger | whether to run cellranger | boolean | True |
Main options¶
| Parameter | Description | Type | Default | Required | Hidden |
|---|---|---|---|---|---|
species | string | hg19 | |||
vars_to_regress | string | ||||
qc_filtering | string | manual | |||
nCount_RNA_max | integer | 500000 | |||
nCount_RNA_min | integer | 1000 | |||
nFeature_RNA_max | integer | 5000 | |||
nFeature_RNA_min | integer | 200 | |||
percent_mt_max | integer | 10 | |||
percent_mt_min | integer | 0 | |||
run_doublet_finder | string | Y | |||
seurat_resolution | string | 0.1,0.2,0.3,0.5,0.6,0.8,1 | |||
npcs | integer | 50 | |||
resolution_list | string | 0.1,0.2,0.3,0.5,0.6,0.8,1 | |||
genome_dir | Path to the genome references. Overridden by platform configs, e.g. conf/biowulf.config | string |
Institutional config options¶
| Parameter | Description | Type | Default | Required | Hidden |
|---|---|---|---|---|---|
config_profile_name | string | ||||
config_profile_description | string | ||||
config_profile_contact | string | ||||
config_profile_url | string |
Generic options¶
| Parameter | Description | Type | Default | Required | Hidden |
|---|---|---|---|---|---|
publish_dir_mode | string | link | True | ||
tracedir | string | ${params.outdir}/pipeline_info | True | ||
max_memory | string | 128.GB | True | ||
max_cpus | integer | 48 | True | ||
max_time | string | 240.h | True |
Containers¶
Docker/Singularity containers to use for processes. Must be available in dockerhub
| Parameter | Description | Type | Default | Required | Hidden |
|---|---|---|---|---|---|
base_container | string | nciccbr/ccbr_ubuntu_base_20.04:v6.1 | True | ||
baser_container | string | nciccbr/sinclair_baser:0.1.0 | True |
Hidden options¶
| Parameter | Description | Type | Default | Required | Hidden |
|---|---|---|---|---|---|
Rlib_dir | string | /gpfs/gsfs10/users/CCBR_Pipeliner/db/PipeDB/Rlibrary_4.3_scRNA_RHEL8 | True | ||
conda_path | string | /gpfs/gsfs10/users/CCBR_Pipeliner/db/PipeDB/Conda/envs/scvi-env | True | ||
python_path | string | /gpfs/gsfs10/users/CCBR_Pipeliner/db/PipeDB/Conda/envs/scvi-env/bin | True | ||
Rpkg | string | ${projectDir}/conf/Rpack.config | True | ||
script_functions | string | ${projectDir}/bin/scRNA_functions.R | True | ||
script_preprocess | string | ${projectDir}/bin/seurat_preprocess.Rmd | True | ||
script_merge | string | ${projectDir}/bin/seurat_merge.Rmd | True | ||
script_bc_harmony | string | ${projectDir}/bin/batch_correction_harmony.Rmd | True | ||
script_bc_rpca | string | ${projectDir}/bin/batch_correction_rpca.Rmd | True | ||
script_bc_cca | string | ${projectDir}/bin/batch_correction_cca.Rmd | True | ||
script_liger | string | ${projectDir}/bin/batch_correction_liger.Rmd | True | ||
script_bc_integration | string | ${projectDir}/bin/batch_correction_integration.Rmd | True |