Add a script to check that all input files are tracked in git

vcs-check.R

@@ -0,0 +1,42 @@
+#!/usr/bin/env Rscript
+
+library(magrittr)
+library(dplyr)
+library(stringr)
+library(processx)
+library(readr)
+
+get_lines <- . %>%
+    str_replace("\n+$", "") %>%
+    str_split_fixed(pattern="\n", n=Inf) %>%
+    as.vector
+
+git_tracked_files <-
+    run("git", c("ls-tree", "-r", "HEAD", "--name-only")) %$%
+    stdout %>% get_lines
+
+snakemake_untracked_files <-
+    run("snakemake", "--list-untracked") %$%
+    stderr %>% get_lines
+
+all_files <- list.files(".", full.names=TRUE, recursive=TRUE) %>%
+    str_replace("^./", "")
+
+snakemake_summary <-
+    run("snakemake", "--summary") %$%
+    stdout %>% read_tsv
+
+snakemake_generated_files <- snakemake_summary$output_file
+
+## All files used as inputs to the snakemake workflow
+input_files <- setdiff(all_files, c(snakemake_untracked_files, snakemake_generated_files))
+
+untracked_input_files <- setdiff(input_files, git_tracked_files) %>% sort
+
+if (length(untracked_input_files) > 0) {
+    message("The following files are used as input but not tracked in git:\n",
+            str_c(untracked_input_files, collapse="\n"))
+    quit(status=1)
+} else {
+    message("All input files used in the workflow are tracked in git.")
+}