snakemake.yml

# It's mandatory to have the references and the mixtures in the same INPUT_FOLDER
# The inputs folder can be obtained from
# /mnt/SERVER-CRCT-STORAGE/CRCT21/Private/Miguel/deconvolutions_pipeline/inputs
INPUT_FOLDER: inputs
OUTPUT_FOLDER: results

# Use your own CBSX credentials here
# https://cibersortx.stanford.edu
# credentials.txt example
# MAIL: registered_mail@mail.com
# TOKEN: c1eac845d51b866b792043a2c964fbe6
# Our team credentials file can be obtained from
# /mnt/SERVER-CRCT-STORAGE/CRCT21/Private/Miguel/deconvolutions_pipeline/credentials.txt>
CREDENTIALS_FILE: credentials.txt

# All mixtures files have to finish with .txt and don't add the .txt here
# It's mandatory to have the references and the mixtures in the same INPUT_FOLDER
# Input mixtures can be obtanined from:
# /mnt/SERVER-CRCT-STORAGE/CRCT21/Private/Miguel/deconvolutions_pipeline/inputs
MIXTURES:
  # - all_TCGA
  # - Melanoma_GSE72056_not_metastatic # Single cell RNA-seq analysis of melanoma Tirosh
  # - Melanoma_GSE93722 #RNA-seq from lymph node bulk samples from 4 melanoma patients.
  # - Silico_1700
  - MultipleMyeloma
  #- GSE1070112 # RNA-Seq profiling of 29 immune cell types and peripheral blood mononuclear cells
  #- salmon


# All references files have to finish with .txt and don't add the .txt here
# It's mandatory to have the references and the mixtures in the same INPUT_FOLDER
# Input mixtures can be obtained from:
# /mnt/SERVER-CRCT-STORAGE/CRCT21/Private/Miguel/deconvolutions_pipeline/inputs
CBSx_SIGNATURES:
  - BPRNACan
  - BPRNACanProMet
  - BPRNACan3DProMet
  - CBSX-HNSCC-scRNAseq
  - CBSX-Melanoma-scRNAseq
  - CBSX-NSCLC-PBMCs-scRNAseq
  - CCLE-TIL10
  - CD226
  - LM22
  - TIL10

channels:
  - conda-forge
dependencies:
  - r=3.4.1
  - r-dplyr
  - r-ggplot2=2.2.1
  - r-gridextra
  - r-reshape2
  - r-readr
  - r-argparse
  - r-viridis
  - r-stringdist
  - r-immunedeconv
  - icu=58.2