feat: bwameth mem and mem2

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

@@ -0,0 +1,91 @@
+# 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 +1,10 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bwameth =0.2.7
+  - bwa-mem2 =2.2.1
+  - 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