feat: bwameth mem and mem2

bio/bwameth/memx/environment.linux-64.pin.txt

@@ -0,0 +1,93 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+# created-by: conda 24.11.0
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
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bio/bwameth/memx/environment.yaml

@@ -0,0 +1,9 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bwameth =0.2.7
+  - samtools =1.21
+  - picard-slim =3.3.0
+  - snakemake-wrapper-utils =0.7.0

bio/bwameth/memx/meta.yaml

@@ -0,0 +1,20 @@
+name: bwa-meth memx
+url: https://github.com/brentp/bwa-meth?tab=readme-ov-file#align
+description: >
+  Align BS-Seq reads on an indexed reference
+authors:
+  - Thibault Dayris
+input:
+  - idx: List of paths to indexed reference files
+  - fq: List of path to fastq files
+  - ref: Path to reference fasta file
+output:
+  - Path to mapped reads (SAM/BAM/CRAM)
+params:
+  - extra: Optional parameters passed to `bwameth.py`, besides IO and threading.
+  - sort: Either `none` (default), `picard`, or `samtools`.
+  - sort_order: Either `coordinate` (default), or `queryname`.
+  - sort_extra: Optional parameters provided to samtools/picard besides IO and threading.
+notes: >
+  Both SAM sorting and compression and handled by either samtools or picard. No duplication analysis is performed by this wrapper.
+

bio/bwameth/memx/test/A.fastq

@@ -0,0 +1,4 @@
+@K00297/1
+AAAAAAAAAAAAAAAAAAAAAAAAA
++
+JJJJJJJJJJJJJJJJJJJJJJJJJ

bio/bwameth/memx/test/Snakefile

@@ -0,0 +1,106 @@
+rule test_bwameth_mem:
+    input:
+        ref="mem/genome.fasta",
+        idx=multiext(
+            "mem/genome.fasta.bwameth",
+            ".c2t",
+            ".c2t.amb",
+            ".c2t.ann",
+            ".c2t.bwt",
+            ".c2t.pac",
+            ".c2t.sa",
+        ),
+        fq=["A.fastq"],
+    output:
+        "A.mem.bam",
+    threads: 2
+    params:
+        extra="",  # Optional parameters for bwameth.py, besides IO and threading
+        sort="none",  # Either `none` (default), `samtools`, or `picard`
+        sort_order="coordinate",  # Either `coordinate` (default) or `queryname`
+        sort_extra="",  # Optional parameters for sambamba/samtools/picard. Ignored if `sort` is equal to `none`.
+    log:
+        "test_bwameth_mem.log"
+    wrapper:
+        "master/bio/bwameth/memx"
+
+
+rule test_bwameth_mem2:
+    input:
+        ref="mem2/genome.fasta",
+        idx=multiext(
+            "mem2/genome.fasta.bwameth",
+            ".c2t",
+            ".c2t.amb",
+            ".c2t.ann",
+            ".c2t.bwt.2bit.64",
+            ".c2t.pac",
+            ".c2t.0123",
+        ),
+        fq=["A.fastq"],
+    output:
+        "A.mem2.bam",
+    threads: 2
+    params:
+        extra="",  # Optional parameters for bwameth.py, besides IO and threading
+        sort="none",  # Either `none` (default), `samtools`, or `picard`
+        sort_order="coordinate",  # Either `coordinate` (default) or `queryname`
+        sort_extra="",  # Optional parameters for sambamba/samtools/picard. Ignored if `sort` is equal to `none`.
+    log:
+        "test_bwameth_mem2.log"
+    wrapper:
+        "master/bio/bwameth/memx"
+
+
+rule test_bwameth_mem_sort_picard:
+    input:
+        ref="mem/genome.fasta",
+        idx=multiext(
+            "mem/genome.fasta.bwameth",
+            ".c2t",
+            ".c2t.amb",
+            ".c2t.ann",
+            ".c2t.bwt",
+            ".c2t.pac",
+            ".c2t.sa",
+        ),
+        fq=["A.fastq"],
+    output:
+        "A.picard_sort.bam",
+    threads: 2
+    params:
+        extra="",  # Optional parameters for bwameth.py, besides IO and threading
+        sort="picard",  # Either `none` (default), `samtools`, or `picard`
+        sort_order="coordinate",  # Either `coordinate` (default) or `queryname`
+        sort_extra="",  # Optional parameters for sambamba/samtools/picard. Ignored if `sort` is equal to `none`.
+    log:
+        "test_bwameth_mem_sort_picard.log"
+    wrapper:
+        "master/bio/bwameth/memx"
+
+
+rule test_bwameth_mem_sort_samtools:
+    input:
+        ref="mem/genome.fasta",
+        idx=multiext(
+            "mem/genome.fasta.bwameth",
+            ".c2t",
+            ".c2t.amb",
+            ".c2t.ann",
+            ".c2t.bwt",
+            ".c2t.pac",
+            ".c2t.sa",
+        ),
+        fq=["A.fastq"],
+    output:
+        "A.samtools_sort.bam",
+    threads: 2
+    params:
+        extra="",  # Optional parameters for bwameth.py, besides IO and threading
+        sort="samtools",  # Either `none` (default), `samtools`, or `picard`
+        sort_order="coordinate",  # Either `coordinate` (default) or `queryname`
+        sort_extra="",  # Optional parameters for sambamba/samtools/picard. Ignored if `sort` is equal to `none`.
+    log:
+        "test_bwameth_mem_sort_samtools.log"
+    wrapper:
+        "master/bio/bwameth/memx"

bio/bwameth/memx/test/mem/genome.fasta

@@ -0,0 +1 @@
+../mem2/genome.fasta

bio/bwameth/memx/test/mem/genome.fasta.bwameth.c2t

@@ -0,0 +1,4 @@
+>rSheila
+ACTAACTCAAAAAAAAAAAA
+>fSheila
+GTTAGTTTAGAAAAAAAAAA

bio/bwameth/memx/test/mem/genome.fasta.bwameth.c2t.amb

@@ -0,0 +1 @@
+40 2 0

bio/bwameth/memx/test/mem/genome.fasta.bwameth.c2t.ann

@@ -0,0 +1,5 @@
+40 2 11
+0 rSheila (null)
+0 20 0
+0 fSheila (null)
+20 20 0

bio/bwameth/memx/test/mem2/genome.fasta

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

bio/bwameth/memx/test/mem2/genome.fasta.bwameth.c2t

@@ -0,0 +1,4 @@
+>rSheila
+ACTAACTCAAAAAAAAAAAA
+>fSheila
+GTTAGTTTAGAAAAAAAAAA

bio/bwameth/memx/test/mem2/genome.fasta.bwameth.c2t.amb

@@ -0,0 +1 @@
+40 2 0

bio/bwameth/memx/test/mem2/genome.fasta.bwameth.c2t.ann

@@ -0,0 +1,5 @@
+40 2 11
+0 rSheila (null)
+0 20 0
+0 fSheila (null)
+20 20 0

bio/bwameth/memx/wrapper.py

@@ -0,0 +1,118 @@
+# coding: utf-8
+
+"""
+Snakemake wrapper for bwameth
+
+Proceeed according to other bwa wrappers: Align + optional sort
+"""
+__author__ = "Thibault Dayris"
+__mail__ = "[email protected]"
+__copyright__ = "Copyright 2024, Thibault Dayris"
+__license__ = "MIT"
+
+import os.path
+import time
+
+from tempfile import TemporaryDirectory
+from snakemake 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("sort", "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)
+
+bwa_threads = snakemake.threads
+samtools_threads = snakemake.threads - 1
+
+# Check arguments
+if sort_order not in {"coordinate", "queryname"}:
+    raise ValueError(f"Unexpected value for sort_order ({sort_order})")
+
+# Determine which pipe command to use for converting to bam or sorting.
+if sort == "none":
+    # Correctly assign number of threads according to user request
+    if samtools_threads >= 1:
+        samtools_opts += f" --threads {samtools_threads} "
+
+    if str(snakemake.output[0]).lower().endswith(("bam", "cram")):
+        # Simply convert to bam using samtools view.
+        pipe_cmd = f" | samtools view {samtools_opts} > {snakemake.output[0]}"
+    else:
+        # Do not perform any sort nor compression, output raw sam
+        pipe_cmd = f" > {snakemake.output[0]} "
+
+
+elif sort == "samtools":
+    # Correctly assign number of threads according to user request
+    if samtools_threads >= 1:
+        samtools_opts += " --threads {samtools_threads} "
+
+    # 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} > {snakemake.output[0]}"
+
+
+elif sort == "picard":
+    # Correctly assign number of threads according to user request
+    bwa_threads -= 1
+    if bwa_threads <= 0:
+        raise ValueError(
+            "Not enough threads requested. This wrapper requires exactly one more."
+        )
+
+    # 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})")
+
+# Gathering fastq files to align
+fq = snakemake.input.get("fq")
+fq1 = snakemake.input.get("fq1")
+fq2 = snakemake.input.get("fq2")
+
+# Single-ended case
+if fq:
+    if isinstance(fq, list):
+        fastq_files = ",".join(fq)
+    else:
+        fastq_files = fq
+
+# Pair-ended case
+elif fq1 and fq2:
+    if isinstance(fq1, list) and isinstance(fq2, list):
+        if len(fq1) == len(fq2):
+            fastq_files = f'{",".join(fq1)} {",".join(fq2)}'
+        else:
+            raise ValueError("Please provide as many R1 and R2 files")
+    else:
+        fastq_files = f"{fq1} {fq2}"
+
+# Missing fastq case
+else:
+    raise ValueError("Either provide `input.fq` or both `input.fq1` and `input.fq2`")
+
+with TemporaryDirectory() as tmpdir:
+    pipe_cmd = pipe_cmd.format(**locals())
+    shell(
+        "(bwameth.py --threads {snakemake.threads} "
+        " {extra} --reference {snakemake.input.ref} "
+        " {fastq_files} {pipe_cmd} ) {log}"
+    )