feat: Add vg giraffe

bio/vg/giraffe/environment.linux-64.pin.txt

@@ -0,0 +1,86 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/bioconda/linux-64/vg-1.60.0-h9ee0642_0.tar.bz2#f66289630d4f712e660657d48b227f06
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bio/vg/giraffe/environment.yaml

@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - vg =1.60
+  - fgbio-minimal =2.3.0
+  - samtools =1.21
+  - picard-slim =3.2.0
+  - snakemake-wrapper-utils =0.6.2

bio/vg/giraffe/meta.yaml

@@ -0,0 +1,16 @@
+name: "vg giraffe"
+description: Map reads using vg giraffe, with optional sorting using
+  samtools or picard.
+url: https://github.com/vgteam/vg
+authors:
+  - Felix Mölder
+input:
+  - FASTQ file(s)
+  - reference graph
+output:
+  - BAM/SAM or CRAM file
+notes: |
+  * The `extra` param allows for additional arguments for vg giraffe.
+  * The `sort_order` params allows sorting by `queryname` or `coordinate`
+  * The `sorting` param allows to enable sorting, and can be either 'none', 'samtools', 'fgbio' or 'picard'.
+  * The `sort_extra` allows for extra arguments for samtools/picard

bio/vg/giraffe/test/Snakefile

@@ -0,0 +1,32 @@
+rule vg_autoindex:  # [hide]
+    input:  # [hide]
+        ref="{genome}.fasta",  # [hide]
+    output:  # [hide]
+        multiext("resources/{genome}", ".dist", ".min", ".giraffe.gbz"),  # [hide]
+    log:  # [hide]
+        "logs/vg_autoindex/{genome}.log",  # [hide]
+    params:  # [hide]
+        extra=r"",  # [hide]
+    threads: 8  # [hide]
+    wrapper:  # [hide]
+        "master/bio/vg/autoindex"  # [hide]
+
+
+rule vg_giraffe_map:
+    input:
+        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
+        graph=f"resources/genome.giraffe.gbz",
+        dist=f"resources/genome.dist",
+        minimizer=f"resources/genome.min",
+    output:
+        "mapped/{sample}.bam",
+    log:
+        "logs/vg_giraffe/{sample}.log",
+    params:
+        extra=r"",
+        sorting="none",  # Can be 'none', 'samtools' or 'picard'.
+        sort_order="queryname",  # Can be 'queryname' or 'coordinate'.
+        sort_extra="",  # Extra args for samtools/picard.
+    threads: 8
+    wrapper:
+        "master/bio/vg/giraffe"

bio/vg/giraffe/test/genome.fasta

@@ -0,0 +1,2 @@
+>Sheila
+GCTAGCTCAGAAAAAAAAAA

bio/vg/giraffe/test/reads/a.1.fastq

@@ -0,0 +1,4 @@
+@1
+ACGGCAT
++
+!!!!!!!

bio/vg/giraffe/test/reads/a.2.fastq

@@ -0,0 +1,4 @@
+@1
+ACGGCAT
++
+!!!!!!!

bio/vg/giraffe/wrapper.py

@@ -0,0 +1,92 @@
+__author__ = "Felix Mölder"
+__copyright__ = "Copyright 2024, Felix Mölder"
+__email__ = "felix.moelder@uk-essen.de"
+__license__ = "MIT"
+
+
+import tempfile
+from os import path
+from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
+from snakemake_wrapper_utils.samtools import get_samtools_opts
+
+
+# Extract arguments.
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+sort = snakemake.params.get("sorting", "none")
+sort_order = snakemake.params.get("sort_order", "coordinate")
+sort_extra = snakemake.params.get("sort_extra", "")
+samtools_opts = get_samtools_opts(snakemake, param_name="sort_extra")
+java_opts = get_java_opts(snakemake)
+
+
+input_cmd = ""
+graph = snakemake.input.graph
+graph_ext = path.splitext(graph)[-1]
+if graph_ext == ".gbz":
+    input_cmd += f"-Z {graph} "
+elif graph_ext == ".xg":
+    input_cmd += f"-x {graph} "
+elif graph_ext == ".gbwt":
+    input_cmd += f"-g {graph} "
+else:
+    raise ValueError("Unexpected file extension for reference graph")
+
+dist_index = snakemake.input.get("dist", None)
+if dist_index:
+    input_cmd += f"-d {dist_index} "
+
+minimizer = snakemake.input.get("minimizer", None)
+if minimizer:
+    input_cmd += f"-m {minimizer}"
+
+
+# Check inputs/arguments.
+if not isinstance(snakemake.input.reads, str) and len(snakemake.input.reads) not in {
+    1,
+    2,
+}:
+    raise ValueError("input must have 1 (single-end) or 2 (paired-end) elements")
+
+reads = (
+    snakemake.input.reads
+    if isinstance(snakemake.input.reads, str)
+    else " -f ".join(snakemake.input.reads)
+)
+
+if sort_order not in {"coordinate", "queryname"}:
+    raise ValueError("Unexpected value for sort_order ({})".format(sort_order))
+
+
+# Determine which pipe command to use for converting to bam or sorting.
+if sort == "none":
+    # Simply convert to bam using samtools view.
+    pipe_cmd = "samtools view {samtools_opts}"
+elif sort == "samtools":
+    # Add name flag if needed.
+    if sort_order == "queryname":
+        sort_extra += " -n"
+    # Sort alignments using samtools sort.
+    pipe_cmd = "samtools sort {samtools_opts} {sort_extra} -T {tmpdir}"
+elif sort == "fgbio":
+    if sort_order == "queryname":
+        sort_extra += " -s Queryname"
+    pipe_cmd = "fgbio SortBam -i /dev/stdin -o {snakemake.output[0]} {sort_extra}"
+elif sort == "picard":
+    # Sort alignments using picard SortSam.
+    pipe_cmd = "picard SortSam {java_opts} {sort_extra} --INPUT /dev/stdin --TMP_DIR {tmpdir} --SORT_ORDER {sort_order} --OUTPUT {snakemake.output[0]}"
+else:
+    raise ValueError(f"Unexpected value for params.sort ({sort})")
+
+
+with tempfile.TemporaryDirectory() as tmpdir:
+    shell(
+        "(vg giraffe"
+        " -t {snakemake.threads}"
+        " {input_cmd}"
+        " -f {reads}"
+        " --output-format BAM"
+        " {extra}"
+        " | " + pipe_cmd + ") {log}"
+    )

test_wrappers.py

@@ -5958,6 +5958,11 @@ def test_vg_construct(run):
         ["snakemake", "--cores", "1", "graph/c.vg", "--use-conda", "-F"],
     )
 
+def test_vg_giraffe(run):
+    run(
+        "bio/vg/giraffe",
+        ["snakemake", "--cores", "1", "mapped/a.bam", "--use-conda", "-F"],
+    )
 
 def test_vg_merge(run):
     run(