mapping_config.yaml

## -------------------- QUICK START ------------------------
# 1. Add organism defaults (e.g. Homo_sapiens.yaml or Mus_musculus.yaml)
# (optional) Overwrite the organism defaults under `organism:`
# 2. Under `pipeline_param:`, configure the paths
# 3. Under `pipeline_param:`, select the steps you wish to run
# 4. Under `report`, enter the meta data (like your name)
# 5. Run `sea-snap sample_info` to generate the sample_info.yaml file
# 5b. To test the configuration, run `sea-snap mapping l -np --cores 1`
# 6. Run `sea-snap mapping l --cores 1` (local, choose how many cores you want) or 
#        `sea-snap mapping --slumr c` (cluster)

## -------------------- PIPELINE CONFIGURATION ------------------------

# 1. --- organism annotation

organism_defaults: ### FILL HERE ###  (e.g. Homo_sapiens.yaml)

  ## See in {sea-snap-directory}/defaults/ for predefined organism files

organism:
  __options__: [name, genus, taxon, files, star_index, salmon_index, R]
  ### OVERWRITE ###  organism defaults (e.g. gtf, genome and indices)


# --- general pipeline parameters

pipeline_param:
  __options__: [out_path_pattern, log_path_pattern, in_path_pattern, mapping_results, QC_results]
  
  # 2. configure the paths

  in_path_pattern: ### FILL HERE ###  (path pattern where fastq files are stored, without fastq.gz extension)
  out_path_pattern: ### FILL HERE ###
  log_path_pattern: ### FILL HERE ###
  # Note: 
  # you need to use every wildcard from `in_path_pattern` both in folder names and file names 
  # of the output patterns.
  #
  # Examples:
  # in_path_pattern: ../fastq/{sample}/{sample}
  # out_path_pattern: mapping/{step}/{sample}/out/{step}.{sample}.{extension}
  # log_path_pattern: mapping/{step}/{sample}/report/{step}.{sample}.{extension}
  #
  # in_path_pattern: input/{sample}/HLFFWDRXX/{lane}/{sample}_{library}_{lane}_{mate}_001
  # out_path_pattern: mapping/{step}/{lane}/{library}/{mate}/{sample}/out/{step}.{lane}.{library}.{mate}.{sample}.{extension}
  # log_path_pattern: mapping/{step}/{lane}/{library}/{mate}/{sample}/report/{step}.{lane}.{library}.{mate}.{sample}.{extension}
  # Default output patterns:
  out_path_pattern: mapping/{step}/{sample}/out/{step}.{sample}.{extension}
  log_path_pattern: mapping/{step}/{sample}/report/{step}.{sample}.{extension}


  # 3. adjust to select which steps to perform
  mapping_results:
    - salmon-transcript_counts
    - star-gene_counts
    - ciri-circRNA
  ## The QC results will be summarized by the multiqc step
  ## You will find the output under  
  ## mapping/multiqc/.../out/multiqc....html
  QC_results:
    - fastqc
    - dupradar
    - infer_experiment
    - qualimap_rnaseq
    - qualimap_bamqc            
    #- rna_seqc
    - preseq_c_curve
    - preseq_lc_extrap
    #- bw_from_bed
    
  #ATAC_Seq:
  #  - macs2


#--- parameters for rules
# See {sea-snap-dir}/defaults/mapping_config_defaults.yaml for more information

rule_options:
  __options__: [star, star_index, salmon, salmon_index]


# 4. --- report settings and metadata
report:
  __options__: [multiqc]
  multiqc:
    report_header_info: ### UNCOMMENT AND FILL (OPTIONAL) ###
    #  - Contact E-mail: '<contact@bihealth.de>'
    #  - Application Type: 'RNA-seq'
    #  - Project Type: '<type>'
    #  - Sequencing Platform: '<platform>'
    #  - Sequencing Setup: '<setup>'
    ## Default output configuration:
    title: SeA-SnaP mapping pipeline QC report
    subtitle: run at the BIH CUBI
    intro_text: The reports summarises results of several QC analyses
    custom_logo: documentation/pictures/SeA-SnaP_logo.png