eQTL-Catalogue/qtlmap output plot data generator workflow

The workflow builds upon Nurlan Kerimov's previous coverage plot workflow and incorporates the logic from Uku Raudvere's eqtl_plot_parsing workflow.

Running the pipeline

nextflow run main.nf -profile tartu_hpc -resume\
  --studyFile ../GEUVADIS_studyfile.tsv\
  --outdir ../GEUVADIS_output

studyFile has to contain columns:

• dataset_id (unique)
• study_id
• quant_method - ge/exon/tx/txrev/leafcutter
• qtl_group - qtl_group in the study
• study_name
• credible_sets_file - File to the credible_sets.parquet file from the qtlmap workflow (./susie/*credible_sets.parquet)
• sample_meta - Sample metadata file. Tab separated file
• vcf_file
• bigwig_path - Path to the bigwig files
• usage_matrix_norm - Path to the normalised usage matrix
• tpm_matrix - Path to the TPM matrix
• exon_summ_stats_files - Path to either (a) a text manifest with one parquet file path per line (no header), or (b) a directory containing exon nominal summary statistics parquet files (*.parquet, non-recursive).
• all_summ_stats_files - Path to either (a) a text manifest with one parquet file path per line (no header), or (b) a directory containing gene nominal summary statistics parquet files (*.parquet, non-recursive).
• pheno_meta - Phenotype metadata file. Tab separated file
• scaling_factors - Path to the scaling_factors file

In nextflow.config file:

• vcf_sample_names_correction — default: false. Set to true to modify sample names in VCF files.
• vcf_samples_old_string_part — default: "". The substring to replace in VCF sample names.
• vcf_samples_new_string_part — default: "". The replacement string for correcting VCF sample names.