Secondary alignments confuse downstream

- Minimap2 includes secondary alignment in its output (useful for
  debugging)
- As spacing-saving feature these do not repeat the SEQ and QUAL from
  the primary alignment
  - This breaks COJAC and SmallGenomeUtilities

workflow/envs/minimap_align.yaml

@@ -3,5 +3,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - minimap2=2.24
-  - samtools=1.10
+  - minimap2=2.26
+  - samtools=1.19

workflow/rules/align.smk

@@ -667,6 +667,9 @@ elif config.general["aligner"] == "minimap":
             SEED="--seed 42",
             EXTRA=config.minimap_align["extra"],
             PRESET=config.minimap_align["preset"],
+            SECONDARY="--secondary=yes --secondary-seq"
+            if config.minimap_align["secondary"]
+            else "--secondary=no",
             FILTER="-f 2" if config.input["paired"] else "-F 4",
             MINIMAP=config.applications["minimap"],
             SAMTOOLS=config.applications["samtools"],

workflow/schemas/config_schema.json

@@ -835,6 +835,12 @@
                     "description": "Specify minimap2 preset options. See [minimape's documentation](https://lh3.github.io/minimap2/minimap2.html#8) for details about each of the presets.",
                     "examples": ["map-ont"]
                 },
+                "secondary": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "By default V-pipe ignores Minimap2's secondary alignment(s) and only considers the primary one (A secondary alignment occurs when a given read could align reasonably well to more than one place). This flags turns back on Minimap2's secondary alignments, and also includes their sequences in the output BAM file.",
+                    "examples": [ true ]
+                },
                 "conda": {
                     "type": "string",
                     "default": "{VPIPE_BASEDIR}/envs/minimap_align.yaml"