diff --git a/bio/vg/giraffe/environment.linux-64.pin.txt b/bio/vg/giraffe/environment.linux-64.pin.txt new file mode 100644 index 00000000000..b26839b02cd --- /dev/null +++ b/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 --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/bioconda/linux-64/vg-1.60.0-h9ee0642_0.tar.bz2#f66289630d4f712e660657d48b227f06 +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda#c27d1c142233b5bc9ca570c6e2e0c244 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda#048b02e3962f066da18efe3a21b77672 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.13-5_cp313.conda#381bbd2a92c863f640a55b6ff3c35161 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2024b-hc8b5060_0.conda#8ac3367aafb1cc0a068483c580af8015 +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda#cc3573974587f12dda90d96e3e55a702 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda#3cb76c3f10d3bc7f1105b2fc9db984df +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.2-heb4867d_0.conda#2b780c0338fc0ffa678ac82c54af51fd +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.3-h5888daf_0.conda#59f4c43bb1b5ef1c71946ff2cbf59524 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_1.conda#e39480b9ca41323497b05492a63bc35b +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.2.0-hc0a3c3a_1.conda#234a5554c53625688d51062645337328 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.2-hb9d3cd8_0.conda#4d638782050ab6faa27275bed57e9b4e +https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda#b3c17d95b5a10c6e64a21fa17573e70e +https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.1-hb9d3cd8_1.conda#19608a9656912805b2b9a2f6bd257b04 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hb9d3cd8_1.conda#77cbc488235ebbaab2b6e912d3934bae +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb9d3cd8_0.conda#8035c64cb77ed555e3f150b7b3972480 +https://conda.anaconda.org/conda-forge/linux-64/xorg-xorgproto-2024.1-hb9d3cd8_1.conda#7c21106b851ec72c037b162c216d8f05 +https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.12-h4ab18f5_0.conda#7ed427f0871fd41cb1d9c17727c17589 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda#3bf7b9fd5a7136126e0234db4b87c8b6 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+https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-hb9d3cd8_2.conda#c9f075ab2f33b3bbee9e62d4ad0a6cd8 +https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb +https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c +https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda#8b189310083baabfb622af68fd9d3ae3 +https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f +https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 +https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.64.0-h161d5f1_0.conda#19e57602824042dfd0446292ef90488b 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+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxtst-1.2.5-hb9d3cd8_3.conda#7bbe9a0cc0df0ac5f5a8ad6d6a11af2f +https://conda.anaconda.org/conda-forge/linux-64/openjdk-22.0.1-h8651b0f_1.conda#672153e7c3d4f70bc65993f3ee513768 +https://conda.anaconda.org/bioconda/linux-64/samtools-1.21-h50ea8bc_0.tar.bz2#4a7fe11223f61cb2d950ed54e20c12ce +https://conda.anaconda.org/bioconda/noarch/fgbio-minimal-2.3.0-hdfd78af_0.tar.bz2#48e39a611203a971c32302c8d0151432 +https://conda.anaconda.org/bioconda/noarch/picard-slim-3.2.0-hdfd78af_0.tar.bz2#b96f183b2167c69b4784ef921bef19ab diff --git a/bio/vg/giraffe/environment.yaml b/bio/vg/giraffe/environment.yaml new file mode 100644 index 00000000000..f30a37b9704 --- /dev/null +++ b/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 diff --git a/bio/vg/giraffe/meta.yaml b/bio/vg/giraffe/meta.yaml new file mode 100644 index 00000000000..b3686f83661 --- /dev/null +++ b/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 diff --git a/bio/vg/giraffe/test/Snakefile b/bio/vg/giraffe/test/Snakefile new file mode 100644 index 00000000000..8b3bb97b032 --- /dev/null +++ b/bio/vg/giraffe/test/Snakefile @@ -0,0 +1,30 @@ +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="", # [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"], + index=multiext("resources/genome", ".dist", ".min", ".giraffe.gbz") + output: + "mapped/{sample}.bam", + log: + "logs/vg_giraffe/{sample}.log", + params: + extra="", + 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" diff --git a/bio/vg/giraffe/test/genome.fasta b/bio/vg/giraffe/test/genome.fasta new file mode 100644 index 00000000000..11d25dda641 --- /dev/null +++ b/bio/vg/giraffe/test/genome.fasta @@ -0,0 +1,2 @@ +>Sheila +GCTAGCTCAGAAAAAAAAAA diff --git a/bio/vg/giraffe/test/reads/a.1.fastq b/bio/vg/giraffe/test/reads/a.1.fastq new file mode 100644 index 00000000000..42735560ae9 --- /dev/null +++ b/bio/vg/giraffe/test/reads/a.1.fastq @@ -0,0 +1,4 @@ +@1 +ACGGCAT ++ +!!!!!!! diff --git a/bio/vg/giraffe/test/reads/a.2.fastq b/bio/vg/giraffe/test/reads/a.2.fastq new file mode 100644 index 00000000000..42735560ae9 --- /dev/null +++ b/bio/vg/giraffe/test/reads/a.2.fastq @@ -0,0 +1,4 @@ +@1 +ACGGCAT ++ +!!!!!!! diff --git a/bio/vg/giraffe/wrapper.py b/bio/vg/giraffe/wrapper.py new file mode 100644 index 00000000000..0dec2cb3082 --- /dev/null +++ b/bio/vg/giraffe/wrapper.py @@ -0,0 +1,81 @@ +__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) + + +expected_files = {".dist": "-d", ".min": "-m", ".giraffe.gbz": "-Z"} + +input_cmd = "" +for ext, param in expected_files.items(): + matching_files = [file for file in snakemake.input.index if file.endswith(ext)] + if not matching_files: + raise ValueError(f"Missing required file with extension: {ext}") + input_cmd += f" {param} {matching_files[0]}" + + +# 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}" + ) diff --git a/test_wrappers.py b/test_wrappers.py index be66914f03c..5c47f4ea9b8 100644 --- a/test_wrappers.py +++ b/test_wrappers.py @@ -5971,6 +5971,11 @@ 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(