fix: Correctly handle non str index list for bwa-mem2/mem (#3101)

As reported in #522, currently the `bwa2-mem` wrapper has issues if
`idx` is a sequence is it incorrectly checked `input.index` to be as
string instead of `input.idx`.

This bug was silent, as usually `snakemake.input.index` would always be
a available as `functools.partial(<function Namedlist._used_attribute at
0x73ac4dbc0c20>, _name='index')` or similar. Thus the predicate that it
was not a `str` was always true.
Now with `snakemake=8.16.0` this changed and the bug becomes an error
running the already existing tests.

While the discussion in #522 indicates, that there is an underlying
issue with the concept of `input.idx` being as sequence of indices, this
may need rework later. Until all the details are decided, having a
correct working version should be still valuable. With the current state
any workflow using this wrapper using `snakemake=8.16.0` is broken.

### QC
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* [x] I confirm that I have followed the [documentation for contributing
to
`snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html).

While the contributions guidelines are more extensive, please
particularly ensure that:
* [x] `test.py` was updated to call any added or updated example rules
in a `Snakefile`
* [x] `input:` and `output:` file paths in the rules can be chosen
arbitrarily
* [x] wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`)
* [x] temporary files are either written to a unique hidden folder in
the working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to
* [x] the `meta.yaml` contains a link to the documentation of the
respective tool or command under `url:`
* [x] conda environments use a minimal amount of channels and packages,
in recommended ordering


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit


- **New Features**
- Enhanced documentation clarifying input requirements for index files,
ensuring users know all necessary file extensions.
- Added a new function to extract the longest common prefix from index
file names, improving error handling.

- **Bug Fixes**
- Updated index file specifications to require a complete list of index
files, preventing execution errors due to missing files.

- **Documentation**
- Improved comments and descriptions in the Snakefile and meta.yaml for
better user guidance on index file usage.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: Vito Zanotelli <vito.zanotelli@gmail.com>

bio/bwa-mem2/mem/meta.yaml

@@ -8,7 +8,10 @@ authors:
   - Thibault Dayris
 input:
   - reads: List of path(s) to FASTQ file(s)
-  - idx: List of paths to indexed reference genome files
+  - idx: |
+     List of paths to indexed reference genome files.
+     All index files required need to be declared:
+     ".0123", ".amb", ".ann", ".bwt.2bit.64", ".pac"
 output:
   - SAM/BAM/CRAM file
 notes: |

bio/bwa-mem2/mem/test/Snakefile

@@ -1,8 +1,8 @@
 rule bwa_mem2_mem:
     input:
         reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
-        # Index can be a list of (all) files created by bwa, or one of them
-        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"),
+        # Index needs to be a list of all index files created by bwa
+        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac", ".0123"),
     output:
         "mapped/{sample}.bam",
     log:
@@ -20,8 +20,8 @@ rule bwa_mem2_mem:
 rule bwa_mem2_mem_sam:
     input:
         reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
-        # Index can be a list of (all) files created by bwa, or one of them
-        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"),
+        # Index needs to be a list of all index files created by bwa
+        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac", ".0123"),
     output:
         "mapped/{sample}.sam",
     log:

bio/bwa-mem2/mem/test/Snakefile_picard

@@ -1,8 +1,8 @@
 rule bwa_mem2_mem:
     input:
         reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
-        # Index can be a list of (all) files created by bwa, or one of them
-        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"),
+        # Index needs to be a list of all index files created by bwa
+        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac", ".0123"),
     output:
         "mapped/{sample}.bam",
     log:

bio/bwa-mem2/mem/test/Snakefile_samtools

@@ -1,8 +1,8 @@
 rule bwa_mem2_mem:
     input:
         reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
-        # Index can be a list of (all) files created by bwa, or one of them
-        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"),
+        # Index needs to be a list of all index files created by bwa
+        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac", ".0123"),
     output:
         "mapped/{sample}.bam",
     log:

bio/bwa-mem2/mem/wrapper.py

@@ -12,6 +12,9 @@
 from snakemake_wrapper_utils.java import get_java_opts
 from snakemake_wrapper_utils.samtools import get_samtools_opts
 
+# All idx required by bwa-mem2
+REQUIRED_IDX = {".0123", ".amb", ".ann", ".bwt.2bit.64", ".pac"}
+
 
 # Extract arguments.
 extra = snakemake.params.get("extra", "")
@@ -27,11 +30,21 @@
 bwa_threads = snakemake.threads
 samtools_threads = snakemake.threads - 1
 
-index = snakemake.input.get("index", "")
-if isinstance(index, str):
-    index = path.splitext(snakemake.input.idx)[0]
-else:
-    index = path.splitext(snakemake.input.idx[0])[0]
+
+# Extract index from input
+# and check that all required indices are declared
+index = path.commonprefix(snakemake.input.idx)[:-1]
+
+if len(index) == 0:
+    raise ValueError("Could not determine common prefix of inputs.idx files.")
+
+index_extensions = [idx[len(index) :] for idx in snakemake.input.idx]
+missing_idx = REQUIRED_IDX - set(index_extensions)
+if len(missing_idx) > 0:
+    raise ValueError(
+        f"Missing required indices: {missing_idx} declarad as input.idx.\n"
+        f"Identified reference file is {index} with extensions {index_extensions}"
+    )
 
 
 # Check inputs/arguments.