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

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(
@@ -4163,7 +4164,19 @@ 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",
+        ],
     )