feat: fixed minimap2 bioconda strict channels, updated version, and a…

…dded test (#527)

* Fixed bioconda strict channels, updated version

* Added extra test

* Point to minor version

* Update bio/minimap2/index/environment.yaml

* Update bio/minimap2/aligner/environment.yaml

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

bio/minimap2/aligner/environment.yaml

@@ -3,5 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - minimap2 ==2.17
-  - samtools ==1.12
+  - minimap2 =2.24
+  - samtools
+  - snakemake-wrapper-utils =0.4

bio/minimap2/aligner/meta.yaml

@@ -1,5 +1,6 @@
 name: minimap2
 description: A versatile pairwise aligner for genomic and spliced nucleotide sequences.
+url: https://lh3.github.io/minimap2
 authors:
   - Tom Poorten
   - Michael Hall
@@ -13,4 +14,3 @@ notes: |
   * The `extra` param allows for additional arguments for minimap2.
   * The `sort` param allows to enable sorting (if output not PAF), and can be either 'none', 'queryname' or 'coordinate'.
   * The `sort_extra` allows for extra arguments for samtools/picard
-  * For more inforamtion see, https://lh3.github.io/minimap2

bio/minimap2/aligner/test/Snakefile

@@ -1,47 +1,66 @@
 rule minimap2_paf:
     input:
-        target="target/{input1}.mmi", # can be either genome index or genome fasta
-        query=["query/reads1.fasta", "query/reads2.fasta"]
+        target="target/{input1}.mmi",  # can be either genome index or genome fasta
+        query=["query/reads1.fasta", "query/reads2.fasta"],
     output:
-        "aligned/{input1}_aln.paf"
+        "aligned/{input1}_aln.paf",
     log:
-        "logs/minimap2/{input1}.log"
+        "logs/minimap2/{input1}.log",
     params:
-        extra="-x map-pb",           # optional
-        sorting="coordinate",           # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
-        sort_extra=""                # optional: extra arguments for samtools/picard
+        extra="-x map-pb",  # optional
+        sorting="coordinate",  # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
+        sort_extra="",  # optional: extra arguments for samtools/picard
     threads: 3
     wrapper:
         "master/bio/minimap2/aligner"
 
+
 rule minimap2_sam:
     input:
-        target="target/{input1}.mmi", # can be either genome index or genome fasta
-        query=["query/reads1.fasta", "query/reads2.fasta"]
+        target="target/{input1}.mmi",  # can be either genome index or genome fasta
+        query=["query/reads1.fasta", "query/reads2.fasta"],
     output:
-        "aligned/{input1}_aln.sam"
+        "aligned/{input1}_aln.sam",
     log:
-        "logs/minimap2/{input1}.log"
+        "logs/minimap2/{input1}.log",
     params:
-        extra="-x map-pb",           # optional
-        sorting="none",                 # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
-        sort_extra=""                # optional: extra arguments for samtools/picard
+        extra="-x map-pb",  # optional
+        sorting="none",  # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
+        sort_extra="",  # optional: extra arguments for samtools/picard
     threads: 3
     wrapper:
         "master/bio/minimap2/aligner"
 
-rule minimap2_bam:
+
+rule minimap2_sam_sorted:
+    input:
+        target="target/{input1}.mmi",  # can be either genome index or genome fasta
+        query=["query/reads1.fasta", "query/reads2.fasta"],
+    output:
+        "aligned/{input1}_aln.sorted.sam",
+    log:
+        "logs/minimap2/{input1}.log",
+    params:
+        extra="-x map-pb",  # optional
+        sorting="queryname",  # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
+        sort_extra="",  # optional: extra arguments for samtools/picard
+    threads: 3
+    wrapper:
+        "master/bio/minimap2/aligner"
+
+
+rule minimap2_bam_sorted:
     input:
-        target="target/{input1}.mmi", # can be either genome index or genome fasta
-        query=["query/reads1.fasta", "query/reads2.fasta"]
+        target="target/{input1}.mmi",  # can be either genome index or genome fasta
+        query=["query/reads1.fasta", "query/reads2.fasta"],
     output:
-        "aligned/{input1}_aln.bam"
+        "aligned/{input1}_aln.sorted.bam",
     log:
-        "logs/minimap2/{input1}.log"
+        "logs/minimap2/{input1}.log",
     params:
-        extra="-x map-pb",           # optional
-        sorting="coordinate",           # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
-        sort_extra=""                # optional: extra arguments for samtools/picard
+        extra="-x map-pb",  # optional
+        sorting="coordinate",  # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
+        sort_extra="",  # optional: extra arguments for samtools/picard
     threads: 3
     wrapper:
         "master/bio/minimap2/aligner"

bio/minimap2/aligner/wrapper.py

@@ -3,23 +3,20 @@
 __email__ = "tom.poorten@gmail.com"
 __license__ = "MIT"
 
+
 from os import path
 from snakemake.shell import shell
+from snakemake_wrapper_utils.samtools import infer_out_format
+from snakemake_wrapper_utils.samtools import get_samtools_opts
 
 
-inputQuery = " ".join(snakemake.input.query)
-
-# Extract output format
-out_name, out_ext = path.splitext(snakemake.output[0])
-out_ext = out_ext[1:].upper()
-
-# Extract arguments.
+samtools_opts = get_samtools_opts(snakemake, parse_output=False)
 extra = snakemake.params.get("extra", "")
-
+log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 sort = snakemake.params.get("sorting", "none")
 sort_extra = snakemake.params.get("sort_extra", "")
 
-log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+out_ext = infer_out_format(snakemake.output[0])
 
 pipe_cmd = ""
 if out_ext != "PAF":
@@ -31,7 +28,7 @@
 
         if out_ext != "SAM":
             # Simply convert to output format using samtools view.
-            pipe_cmd = "| samtools view -h --output-fmt {} -".format(out_ext)
+            pipe_cmd = f"| samtools view -h {samtools_opts}"
 
     elif sort in ["coordinate", "queryname"]:
 
@@ -40,13 +37,19 @@
             sort_extra += " -n"
 
         # Sort alignments.
-        pipe_cmd = "| samtools sort {} --output-fmt {} -".format(sort_extra, out_ext)
+        pipe_cmd = f"| samtools sort {sort_extra} {samtools_opts}"
 
     else:
-        raise ValueError("Unexpected value for params.sort ({})".format(sort))
+        raise ValueError(f"Unexpected value for params.sort: {sort}")
 
 
 shell(
-    "(minimap2 -t {snakemake.threads} {extra} "
-    "{snakemake.input.target} {inputQuery} {pipe_cmd} > {snakemake.output[0]}) {log}"
+    "(minimap2"
+    " -t {snakemake.threads}"
+    " {extra} "
+    " {snakemake.input.target}"
+    " {snakemake.input.query}"
+    " {pipe_cmd}"
+    " > {snakemake.output[0]}"
+    ") {log}"
 )

bio/minimap2/index/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - minimap2 ==2.17
+  - minimap2 =2.24

bio/minimap2/index/meta.yaml

@@ -1,4 +1,9 @@
 name: minimap2 index
 description: creates a minimap2 index
+url: https://lh3.github.io/minimap2
 authors:
   - Tom Poorten
+input:
+  - reference genome in FASTA format
+output:
+  - indexed reference genome

test.py

@@ -2290,10 +2290,18 @@ def test_minimap2_aligner_sam():
 
 
 @skip_if_not_modified
-def test_minimap2_aligner_bam():
+def test_minimap2_aligner_sam_sorted():
     run(
         "bio/minimap2/aligner",
-        ["snakemake", "--cores", "1", "aligned/genome_aln.bam", "--use-conda", "-F"],
+        ["snakemake", "--cores", "1", "aligned/genome_aln.sorted.sam", "--use-conda", "-F"],
+    )
+
+
+@skip_if_not_modified
+def test_minimap2_aligner_bam_sorted():
+    run(
+        "bio/minimap2/aligner",
+        ["snakemake", "--cores", "1", "aligned/genome_aln.sorted.bam", "--use-conda", "-F"],
     )