Also convert DiscardCasava

src/cutadapt/cli.py

@@ -98,6 +98,7 @@
     TooManyN,
     TooManyExpectedErrors,
     TooHighAverageErrorRate,
+    CasavaFiltered,
 )
 from cutadapt.report import full_report, minimal_report, Statistics
 from cutadapt.pipeline import SingleEndPipeline, PairedEndPipeline
@@ -932,6 +933,16 @@ def make_pipeline_from_args(  # noqa: C901
                 step = SingleEndFilter(predicate, None)
             steps.append(step)
 
+    if args.discard_casava:
+        predicate = CasavaFiltered()
+        if paired:
+            step = PairedEndFilter(
+                predicate, predicate, writer=None, pair_filter_mode=pair_filter_mode
+            )
+        else:
+            step = SingleEndFilter(predicate, None)
+        steps.append(step)
+
     logger.debug("Pipeline steps:")
     for step in steps:
         logger.debug("- %s", step)
@@ -1013,7 +1024,6 @@ def make_pipeline_from_args(  # noqa: C901
         pipeline.override_untrimmed_pair_filter = True
 
     # Set filtering parameters
-    pipeline.discard_casava = args.discard_casava
     pipeline.discard_trimmed = args.discard_trimmed
     pipeline.discard_untrimmed = args.discard_untrimmed
 

src/cutadapt/pipeline.py

@@ -25,7 +25,6 @@
 from .predicates import (
     DiscardUntrimmed,
     Predicate,
-    CasavaFiltered,
     DiscardTrimmed,
 )
 from .steps import (
@@ -61,7 +60,6 @@ def __init__(self) -> None:
         self._textiowrappers: List[TextIO] = []
 
         # Filter settings
-        self.discard_casava = False
         self.discard_trimmed = False
         self.discard_untrimmed = False
 
@@ -96,10 +94,6 @@ def _set_output(self, outfiles: OutputFiles) -> None:  # noqa: C901
         steps = []
         files: List[Optional[BinaryIO]]
 
-        if self.discard_casava:
-            f1 = f2 = CasavaFiltered()
-            steps.append(self._make_filter(f1, f2, None))
-
         if (
             int(self.discard_trimmed)
             + int(self.discard_untrimmed)