config.yaml

##### input information #####
# Sample info. Includes: reference (path), gtf (path), allSamples (bool), Controls (bool)
mapping_sample: aireTrace
samples:
    aireTrace:
        reference:
            /home/kwells4/kwells4/cellranger/mm10_GFP_RFP
        gtf:
            /home/kwells4/kwells4/cellranger/mm10_GFP_RFP/genes/genes.gtf
        allSamples:
            True
        Controls:
            False
    isoControlBeg:
        reference:
            /home/kwells4/kwells4/cellranger/refdata-cellranger-mm10-1.2.0
        gtf:
            /home/kwells4/kwells4/cellranger/refdata-cellranger-mm10-1.2.0/genes/genes.gtf
        allSamples:
            True
        Controls:
            True
    timepoint1:
        reference:
            /home/kwells4/kwells4/cellranger/refdata-cellranger-mm10-1.2.0
        gtf:
            /home/kwells4/kwells4/cellranger/refdata-cellranger-mm10-1.2.0/genes/genes.gtf
        allSamples:
            True
        Controls:
            False
    timepoint2:
        reference:
            /home/kwells4/kwells4/cellranger/refdata-cellranger-mm10-1.2.0
        gtf:
            /home/kwells4/kwells4/cellranger/refdata-cellranger-mm10-1.2.0/genes/genes.gtf
        allSamples:
            True
        Controls:
            False
    timepoint3:
        reference:
            /home/kwells4/kwells4/cellranger/refdata-cellranger-mm10-1.2.0
        gtf:
            /home/kwells4/kwells4/cellranger/refdata-cellranger-mm10-1.2.0/genes/genes.gtf
        allSamples:
            True
        Controls:
            False
    timepoint5:
        reference:
            /home/kwells4/kwells4/cellranger/refdata-cellranger-mm10-1.2.0
        gtf:
            /home/kwells4/kwells4/cellranger/refdata-cellranger-mm10-1.2.0/genes/genes.gtf
        allSamples:
            True
        Controls:
            False
    isoControlEnd:
        reference:
            /home/kwells4/kwells4/cellranger/refdata-cellranger-mm10-1.2.0
        gtf:
            /home/kwells4/kwells4/cellranger/refdata-cellranger-mm10-1.2.0/genes/genes.gtf
        allSamples:
            True
        Controls:
            True

# seurat project name
project: RankL_ablation

# Path to data_dir
data_dir: /home/kwells4/mTEC_dev/data/

# memory to allow cell ranger to use
mem: 100

# All files required to make the figure. Paths relative to the directory containing the
# Snakefile. Add in progenitor file
fig_files:
    - aireTrace/analysis_outs/seurat_aireTrace.rda
    - controls/analysis_outs/seurat_controls_merged.rda
    - allSamples/analysis_outs/seurat_allSamples_combined.rda
    - controls/analysis_outs/controls_merged_slingshot.rda
    - allSamples/analysis_outs/allSamples_combined_slingshot.rda
    - allSamples/analysis_outs/seurat_allSamples_Early_Aire_combined.rda