After the update, dialoguer doesn't show the prompt anymore, so can't…

… test.

src/file_io.rs

@@ -84,9 +84,10 @@ pub fn create_writer(
     if *compress {
         let writer = ZBuilder::<Gzip, _>::new()
             .num_threads(*num_threads)
-            .compression_level(compression_level.map_or_else(Default::default, |l| {
-                Compression::new((l).clamp(1, 9))
-            }))
+            .compression_level(
+                compression_level
+                    .map_or_else(Default::default, |l| Compression::new((l).clamp(1, 9))),
+            )
             .pin_threads(pin_at)
             .from_writer(file);
         Ok(OutputFile::Compressed(FastqWriter::from_bufwriter(

src/main.rs

@@ -25,7 +25,7 @@ https://github.com/SciLifeLab/umi-transfer
 
 #[derive(clap::Parser)]
 #[clap(
-    version = "1.0.0",
+    version = "1.5.0dev",
     author = "Written by Judit Hohenthal, Matthias Zepper & Johannes Alneberg",
     about = "A tool for transferring Unique Molecular Identifiers (UMIs).",
     long_about = "Most tools capable of using UMIs to increase the accuracy of quantitative DNA sequencing experiments expect the respective UMI sequence to be embedded into the reads' IDs. You can use `umi-transfer external` to retrieve UMIs from a separate FastQ file and embed them to the IDs of your paired FastQ files."

tests/integration_tests_external.rs

@@ -220,9 +220,9 @@ fn external_fails_with_existing_output_file_and_no_force() {
     cmd.assert()
         .failure()
         .stderr(predicate::str::contains("Failed to include the UMIs"))
-        .stderr(predicate::str::contains("Caused by:"))
-        .stderr(predicate::str::contains("exists. Overwrite? (y/n)"))
-        .stderr(predicate::str::contains("Not a terminal"));
+        //.stderr(predicate::str::contains("Caused by:"))
+        //.stderr(predicate::str::contains("exists. Overwrite? (y/n)"))
+        .stderr(predicate::str::contains("not a terminal"));
 
     temp_dir
         .child("read2_out.fq")