Config validation function checks everything

[danielsarj]

In an attempt to run a dry-run with another test dataset, an error occurs:

$ snakemake-run-cellranger run --config-file /project/lbarreiro/USERS/daniel/cellranger-snakemake_PBMCtest/pipeline_config.yaml --cores 1 --dry-run
Warning: Ignoring unused demultiplexing configs: ['vireo']
[INFO] Config validated. Enabled steps: cellranger_gex, doublet_detection
[INFO] Running Snakemake with command: snakemake --snakefile /project/lbarreiro/USERS/daniel/cellranger-snakemake/cellranger_snakemake/workflows/main.smk --configfile /project/lbarreiro/USERS/daniel/cellranger-snakemake_PBMCtest/pipeline_config.yaml --cores 1 --use-conda --dry-run
[INFO] ============================================================
[INFO] Single-Cell Preprocessing Pipeline
[INFO] ============================================================
[INFO] Project: 10k_pbmc
[INFO] Output directory: 10k_pbmc_output
[INFO] Enabled steps: cellranger_gex, doublet_detection
[INFO] ============================================================
[INFO] /project/lbarreiro/USERS/daniel/cellranger-snakemake_PBMCtest/libraries_list_gex.tsv file format is valid.
[INFO] /project/lbarreiro/USERS/daniel/cellranger-snakemake_PBMCtest/libraries_list_gex.tsv file format is valid.
[INFO] Cell Ranger GEX: Found 1 sample(s) across 1 batch(es)
[INFO] Cell Ranger GEX: Found 1 sample(s) across 1 batch(es)
[ERROR] Pandas could not read your libraries filepath here: 'libraries_atac.tsv'. This was the error: [Errno 2] No such file or directory: 'libraries_atac.tsv'
[ERROR] Pandas could not read your libraries filepath here: 'libraries_atac.tsv'. This was the error: [Errno 2] No such file or directory: 'libraries_atac.tsv'

It seems that the current config validation function will check everything in the config regardless of what is turned on. As you can see, the config file I used has only "gex" set to true:

cellranger_gex:
  enabled: true
  reference: /project/lbarreiro/USERS/daniel/cellranger-snakemake_PBMCtest/refdata-gex-GRCh38-2020-A
  libraries: /project/lbarreiro/USERS/daniel/cellranger-snakemake_PBMCtest/libraries_list_gex.tsv
  chemistry: auto
  normalize: none
  create-bam: false
  threads: 10
  mem_gb: 64
  directories:
    LOGS_DIR: 00_LOGS
cellranger_atac:
  enabled: false
  reference: /path/to/cellranger-atac/reference
  libraries: libraries_atac.tsv
  chemistry: auto
  normalize: none
  threads: 10
  mem_gb: 64
  directories:
    LOGS_DIR: 00_LOGS
cellranger_arc:
  enabled: false
  reference: /path/to/cellranger-arc/reference
  libraries: libraries_arc.tsv
  normalize: none
  directories:
    LOGS_DIR: 00_LOGS
  threads: 10
  mem_gb: 64