keep everything seperate

Snakefile

@@ -10,15 +10,7 @@ localrules: impute, clean, download_container, generate_samples_file
 rule impute:
     input:
         "container.sif",
-        expand("{output_dir}/imputed-gene-expressions/{region}.expression.txt", region = config['brain_regions'], output_dir = config['output_dir'])
-    output:
-        expand("{output_dir}/imputed-gene-expressionss_combined.rds", output_dir = config['output_dir'])
-    singularity:
-        "container.sif"
-    shell:
-        """
-        Rscript scripts/combine_expression_data.R
-        """
+        expand("{output_dir}/imputed-gene-expressions/{region}.expression.txt.gz", region = config['brain_regions'], output_dir = config['output_dir'])
 
 # delete output and logs (if run on slurm cluster)
 rule clean:
@@ -108,9 +100,12 @@ rule impute_gene_expressions:
     input:
         "container.sif",
         samples_file = expand("{output_dir}/dosages/samples.txt", output_dir = config['output_dir']),
-        dosage_files = expand("{output_dir}/dosages/chr{i}.dosage.txt.gz", i = range(1, 23), output_dir = config['output_dir'])
+        dosage_files = expand("{output_dir}/dosages/chr{i}.dosage.txt.gz",
+            i = list(map(str, range(1, 23))) + ['X'],
+            output_dir = config['output_dir']
+        )
     output:
-        "{output_dir}/imputed-gene-expressions/{region}.expression.txt"
+        "{output_dir}/imputed-gene-expressions/{region}.expression.txt.gz"
     singularity:
         "container.sif"
     shell:
@@ -125,4 +120,5 @@ rule impute_gene_expressions:
             --output_prefix {wildcards.output_dir}/imputed-gene-expressions/{wildcards.region}
         mv {wildcards.output_dir}/imputed-gene-expressions/{wildcards.region}_predicted_expression.txt \
             {wildcards.output_dir}/imputed-gene-expressions/{wildcards.region}.expression.txt
+        gzip {wildcards.output_dir}/imputed-gene-expressions/{wildcards.region}.expression.txt
         """

scripts/combine_expression_data.R

-#!/usr/bin/env Rscript
-
-library(dplyr, warn.conflicts = FALSE)
-library(readr, warn.conflicts = FALSE)
-
-config <- yaml::read_yaml('config.yml')
-
-col_types  <- cols(
-    .default = col_double(),
-    FID      = col_character(),
-    IID      = col_character()
-)
-
-# read and combine individual expression data in long format
-config$brain_regions %>%
-    purrr::map(
-        function(x) {
-            sprintf("%s/imputed-gene-expressions/%s.expression.txt", config$output_dir, x) %>%
-                read_tsv(col_types = col_types, progress = FALSE) %>%
-                tidyr::gather('ensembl_gene_id', 'expression', -FID, -IID) %>%
-                mutate(tissue = x) %>%
-                select(tissue, everything())
-        }
-    ) %>%
-    {do.call(rbind, .)} %>%
-    # make missing genes explicit
-    tidyr::spread(ensembl_gene_id, expression, fill = NA_real_) %>%
-    tidyr::gather('ensembl_gene_id', 'expression', -FID, -IID, -tissue) %>%
-    write_rds(sprintf('%s/imputed-gene-expressionss_combined.rds', config$output_dir), compress = 'gz')