feat: Bowtie2 meta

meta/bio/bowtie2_sambamba/meta.yaml

@@ -0,0 +1,22 @@
+name: Bowtie2 Sambamba
+url: http://lomereiter.github.io/sambamba/
+description: >
+  Map reads with Bowtie 2, and post-process alignments with Sambamba.
+
+  +----------------+----------+----------------------------------------------------------------------------------------------+
+  | Step           | Tool     | Reason                                                                                       |
+  +================+==========+==============================================================================================+
+  | Indexation     | Bowtie 2 | Create genome sequence index                                                                 |
+  +----------------+----------+----------------------------------------------------------------------------------------------+
+  | Mapping        | Bowtie 2 | Perform read mapping                                                                         |
+  +----------------+----------+----------------------------------------------------------------------------------------------+
+  | Sort           | Sambamba | Perform sort based on mapping position                                                       |
+  +----------------+----------+----------------------------------------------------------------------------------------------+
+  | Quality filter | Sambamba | Perform mapping quality filter                                                               |
+  +----------------+----------+----------------------------------------------------------------------------------------------+
+  | Deduplication  | Sambamba | Identify possible sequencing duplicates                                                      |
+  +----------------+----------+----------------------------------------------------------------------------------------------+
+  | Indexation     | Sambamba | Index deduplicated reads                                                                     |
+  +----------------+----------+----------------------------------------------------------------------------------------------+
+authors:
+  - Thibault Dayris

meta/bio/bowtie2_sambamba/test/Sample1.R1.fastq

@@ -0,0 +1,32 @@
+@1
+GCTGCTATGGCTATAGCTCTA
++
+IIIIIIIIIIIIIIIIIIIII
+@2
+GCTGCTATGGCTATAGCTCTA
++
+IIIIIIIIIIIIIIIIIIIII
+@3
+GCTGCTATGGCTATAGCTCTA
++
+IIIIIIIIIIIIIIIIIIIII
+@4
+GCTGCTATGGCTATAGCTCTA
++
+IIIIIIIIIIIIIIIIIIIII
+@5
+GCTGCTATGGCTATAGCTCTA
++
+IIIIIIIIIIIIIIIIIIIII
+@6
+GCTGCTATGGCTATAGCTCTA
++
+IIIIIIIIIIIIIIIIIIIII
+@7
+GCTGCTATGGCTATAGCTCTA
++
+IIIIIIIIIIIIIIIIIIIII
+@8
+GTATCGATCCGATTA
++
+IIIIIIIIIIIIIII

meta/bio/bowtie2_sambamba/test/Sample1.R2.fastq

@@ -0,0 +1,32 @@
+@1
+CTCGATATCGCGCTACGATCC
++
+IIIIIIIIIIIIIIIIIIIII
+@2
+CTCGATATCGCGCTACGATCC
++
+IIIIIIIIIIIIIIIIIIIII
+@3
+CTCGATATCGCGCTACGATCC
++
+IIIIIIIIIIIIIIIIIIIII
+@4
+CTCGATATCGCGCTACGATCC
++
+IIIIIIIIIIIIIIIIIIIII
+@5
+CTCGATATCGCGCTACGATCC
++
+IIIIIIIIIIIIIIIIIIIII
+@6
+CTCGATATCGCGCTACGATCC
++
+IIIIIIIIIIIIIIIIIIIII
+@7
+CTCGATATCGCGCTACGATCC
++
+IIIIIIIIIIIIIIIIIIIII
+@8
+ATATCGATCGACGAT
++
+IIIIIIIIIIIIIII

meta/bio/bowtie2_sambamba/test/Snakefile

@@ -0,0 +1,105 @@
+rule bowtie2_build:
+    input:
+        ref="genome.fasta",
+    output:
+        multiext(
+            "genome",
+            ".1.bt2",
+            ".2.bt2",
+            ".3.bt2",
+            ".4.bt2",
+            ".rev.1.bt2",
+            ".rev.2.bt2",
+        ),
+    log:
+        "logs/bowtie2_build/build.log",
+    params:
+        extra="",
+    threads: 8
+    wrapper:
+        "master/bio/bowtie2/build"
+
+
+rule bowtie2_alignment:
+    input:
+        sample=["{sample}.R1.fastq", "{sample}.R2.fastq"],
+        idx=multiext(
+            "genome",
+            ".1.bt2",
+            ".2.bt2",
+            ".3.bt2",
+            ".4.bt2",
+            ".rev.1.bt2",
+            ".rev.2.bt2",
+        ),
+    output:
+        temp("mapped/{sample}.bam"),
+    log:
+        "logs/bowtie2/{sample}.log",
+    params:
+        extra=(
+            " --rg-id {sample} "
+            "--rg 'SM:{sample} LB:FakeLib PU:FakePU.1.{sample} PL:ILLUMINA' "
+        ),
+    threads: 8
+    wrapper:
+        "master/bio/bowtie2/align"
+
+
+rule sambamba_sort:
+    input:
+        "mapped/{sample}.bam",
+    output:
+        temp("mapped/{sample}.sorted.bam"),
+    params:
+        "",
+    log:
+        "logs/sambamba-sort/{sample}.log",
+    threads: 8
+    wrapper:
+        "master/bio/sambamba/sort"
+
+
+rule sambamba_view:
+    input:
+        "mapped/{sample}.sorted.bam",
+    output:
+        temp("mapped/{sample}.filtered.bam"),
+    params:
+        extra=(
+            " --format 'bam' "
+            "--filter 'mapping_quality >= 30 and not (unmapped or mate_is_unmapped)' "
+        ),
+    log:
+        "logs/sambamba-view/{sample}.log",
+    threads: 8
+    wrapper:
+        "master/bio/sambamba/view"
+
+
+rule sambamba_markdup:
+    input:
+        "mapped/{sample}.filtered.bam",
+    output:
+        "mapped/{sample}.rmdup.bam",
+    params:
+        extra=" --remove-duplicates ",  # optional parameters
+    log:
+        "logs/sambamba-markdup/{sample}.log",
+    threads: 8
+    wrapper:
+        "master/bio/sambamba/markdup"
+
+
+rule sambamba_index:
+    input:
+        "mapped/{sample}.rmdup.bam",
+    output:
+        "mapped/{sample}.rmdup.bam.bai",
+    params:
+        extra="",
+    log:
+        "logs/sambamba-index/{sample}.log",
+    threads: 8
+    wrapper:
+        "master/bio/sambamba/index"

meta/bio/bowtie2_sambamba/test/genome.fasta

@@ -0,0 +1,3 @@
+>FakeChrom
+ATCGATGCTGCTATAGCTATAGCTCTAGATCTGATCTGCTAGTATCGATCCGATTATTAGCGCGATTATAGCGTAGTCA
+ATCGATCTCGATATCGCGCTACGATCCGCGCGCGCGCGCGCATTATATCGATCGACGATGCTGCTAGCTAGCTGCTAGC

meta/bio/bowtie2_sambamba/used_wrappers.yaml

@@ -0,0 +1,7 @@
+wrappers:
+  - bio/bowtie2/build
+  - bio/bowtie2/align
+  - bio/sambamba/sort
+  - bio/sambamba/view
+  - bio/sambamba/markdup
+  - bio/sambamba/index

test.py

@@ -5688,6 +5688,22 @@ def test_calc_consensus_reads():
     )
 
 
+
+@skip_if_not_modified
+def test_bowtie2_sambamba_meta():
+    run(
+        "meta/bio/bowtie2_sambamba",
+        [
+            "snakemake",
+            "--cores",
+            "2",
+            "--use-conda",
+            "-F",
+            "mapped/Sample1.rmdup.bam.bai"
+        ]
+    )
+
+
 @skip_if_not_modified
 def test_bazam_interleaved():
     run(