feat: Add support for regions file and arbitrary FAI/GZI paths (snake…

…make#2936)

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### QC
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* [x] I confirm that:

For all wrappers added by this PR, 

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* 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 (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).

---------

Co-authored-by: Christian Meesters <[email protected]>

bio/samtools/faidx/meta.yaml

@@ -1,12 +1,18 @@
 name: samtools faidx
 description: index reference sequence in FASTA format from reference sequence.
+url: http://www.htslib.org/doc/samtools-faidx.html
 authors:
   - Michael Chambers
   - Filipe G. Vieira
 input:
   - reference sequence file (.fa)
+  - regions: file with regions
+  - fai: index for reference file (optional)
+  - gzi: index for BGZip'ed reference file (optional)
 output:
   - indexed reference sequence file (.fai)
-notes: |
-  * The `extra` param allows for additional program arguments (not `-o`).
-  * For more information see, http://www.htslib.org/doc/samtools-faidx.html
+  - fai: index for reference file (optional)
+  - gzi: index for BGZip'ed reference file (optional)
+params:
+  - region: region to extract from input file (optional)
+  - extra: additional program arguments (not `-o`).

bio/samtools/faidx/test/Snakefile

@@ -1,11 +1,69 @@
-rule samtools_index:
+rule samtools_faidx:
     input:
         "{sample}.fa",
     output:
-        "{sample}.fa.fai",
+        "out/{sample}.fa.fai",
     log:
         "{sample}.log",
     params:
-        extra="",  # optional params string
+        extra="",
+    wrapper:
+        "master/bio/samtools/faidx"
+
+
+rule samtools_faidx_named:
+    input:
+        "{sample}.fa",
+    output:
+        fai="out/{sample}.named.fa.fai",
+    log:
+        "{sample}.named.log",
+    params:
+        extra="",
+    wrapper:
+        "master/bio/samtools/faidx"
+
+
+rule samtools_faidx_bgzip:
+    input:
+        "{sample}.fa.bgz",
+    output:
+        fai="out/{sample}.fas.bgz.fai",
+        gzi="out/{sample}.fas.bgz.gzi",
+    log:
+        "{sample}.bzgip.log",
+    params:
+        extra="",
+    wrapper:
+        "master/bio/samtools/faidx"
+
+
+rule samtools_faidx_region:
+    input:
+        "{sample}.fa",
+        fai="idx/{sample}.fa.fai",
+    output:
+        "out/{sample}.fas",
+    log:
+        "{sample}.region.log",
+    params:
+        region="ref",
+        extra="--length 5",
+    wrapper:
+        "master/bio/samtools/faidx"
+
+
+rule samtools_faidx_bgzip_region:
+    input:
+        "{sample}.fa.bgz",
+        fai="idx/{sample}.fa.bgz.fai",
+        gzi="idx/{sample}.fa.bgz.gzi",
+    output:
+        "out/{sample}.bgz.fas",
+    log:
+        "{sample}.bgzip_region.log",
+    params:
+        region="ref",
+        extra="--length 5",
     wrapper:
         "master/bio/samtools/faidx"

bio/samtools/faidx/test/idx/genome.fa.bgz.fai

@@ -0,0 +1,2 @@
+ref	45	5	45	46
+ref2	40	57	40	41

bio/samtools/faidx/test/idx/genome.fa.fai

@@ -0,0 +1,2 @@
+ref	45	5	45	46
+ref2	40	57	40	41

bio/samtools/faidx/wrapper.py

@@ -13,4 +13,28 @@
 extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
-shell("samtools faidx {samtools_opts} {extra} {snakemake.input[0]} {log}")
+
+# Get regions (if present)
+regions = snakemake.input.get("regions", "")
+if regions:
+    regions = f"--regions-file {regions}"
+
+region = snakemake.params.get("region", "")
+
+# Get FAI and GZI files
+if region or regions:
+    fai = snakemake.input.get("fai", "")
+    gzi = snakemake.input.get("gzi", "")
+else:
+    fai = snakemake.output.get("fai", "")
+    gzi = snakemake.output.get("gzi", "")
+
+if fai:
+    fai = f"--fai-idx {fai}"
+if gzi:
+    gzi = f"--gzi-idx {gzi}"
+
+
+shell(
+    "samtools faidx {fai} {gzi} {regions} {samtools_opts} {extra} {snakemake.input[0]} {region:q} {log}"
+)

test.py

@@ -1453,6 +1453,7 @@ def test_goleft_indexcov():
         ["snakemake", "--cores", "1", "--use-conda", "-Fp"],
     )
 
+
 @skip_if_not_modified
 def test_gridss_call():
     run(
@@ -4171,7 +4172,19 @@ def test_samtools_fastq_separate():
 def test_samtools_faidx():
     run(
         "bio/samtools/faidx",
-        ["snakemake", "--cores", "1", "genome.fa.fai", "--use-conda", "-F"],
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "out/genome.fa.fai",
+            "out/genome.named.fa.fai",
+            "out/genome.fas.bgz.fai",
+            "out/genome.fas.bgz.gzi",
+            "out/genome.fas",
+            "out/genome.bgz.fas",
+            "--use-conda",
+            "-F",
+        ],
     )