feat: explicitly specify bwa index in bwa wrappers (#232)

* [fix] (template): Missing code in wrappers' doc. Error #187

* [dev] (bwa): Automatic prefix detection (#228)

* [dev] (bwa): Automatix prefix detection (#228)

* [doc] (bwa): Snakefiles updated

* [dev] (bwa): Aln was forgotten at first

* [dev] (black): Reformatting

* Update Snakefile_samtools

* minimal formatting commit to trigger tests

test logs are not available any more

* revert test trigger change

* feat!: remove tmp dir parameter in bwa mem wrapper as this is now handled automatically by snakemake

* fix: fixed index adressing

* fmt

* fixes

* fixes

* fixed failing lint, fixed syntax

* add missing logfile

Co-authored-by: tdayris <tdayris@gustaveroussy.fr>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

bio/bwa-mem2/index/test/Snakefile

@@ -1,15 +1,15 @@
 rule bwa_mem2_index:
     input:
-        "{genome}"
+        "{genome}",
     output:
         "{genome}.0123",
         "{genome}.amb",
         "{genome}.ann",
         "{genome}.bwt.2bit.64",
         "{genome}.pac",
     log:
-        "logs/bwa-mem2_index/{genome}.log"
+        "logs/bwa-mem2_index/{genome}.log",
     params:
-        prefix=lambda w: w.genome
+        prefix=lambda w: w.genome,
     wrapper:
         "master/bio/bwa-mem2/index"

bio/bwa-mem2/index/wrapper.py

@@ -16,7 +16,11 @@
     raise ValueError("Please provide exactly one reference genome as input.")
 
 # Prefix that should be used for the database
-prefix = snakemake.params.get("prefix", "")
+prefix = None
+if "prefix" in snakemake.params.keys():
+    prefix = snakemake.params["prefix"]
+else:
+    prefix = splitext(snakemake.output[0])[0]
 
 if len(prefix) > 0:
     prefix = "-p " + prefix

bio/bwa-mem2/mem-samblaster/test/Snakefile

@@ -1,15 +1,16 @@
 rule bwa_mem:
     input:
-        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"]
+        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
+        # Index can be a list of (all) files created by bwa, or one of them
+        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"),
     output:
         bam="mapped/{sample}.bam",
-        index="mapped/{sample}.bam.bai"
+        index="mapped/{sample}.bam.bai",
     log:
-        "logs/bwa_mem2_sambamba/{sample}.log"
+        "logs/bwa_mem2_sambamba/{sample}.log",
     params:
-        index="genome.fasta",
         extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
-        sort_extra="-q" # Extra args for sambamba.
+        sort_extra="-q",  # Extra args for sambamba.
     threads: 8
     wrapper:
         "master/bio/bwa-mem2/mem-samblaster"

bio/bwa-mem2/mem-samblaster/wrapper.py

@@ -14,6 +14,12 @@
 sort_extra = snakemake.params.get("sort_extra", "")
 samblaster_extra = snakemake.params.get("samblaster_extra", "")
 
+index = snakemake.input.get("index", "")
+if isinstance(index, str):
+    index = path.splitext(snakemake.input.idx)[0]
+else:
+    index = path.splitext(snakemake.input.idx[0])[0]
+
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 
 # Check inputs/arguments.
@@ -27,7 +33,7 @@
     "(bwa-mem2 mem"
     " -t {snakemake.threads}"
     " {extra}"
-    " {snakemake.params.index}"
+    " {index}"
     " {snakemake.input.reads}"
     " | samblaster"
     " {samblaster_extra}"

bio/bwa-mem2/mem/test/Snakefile

@@ -1,16 +1,17 @@
 rule bwa_mem2_mem:
     input:
-        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"]
+        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
+        # Index can be a list of (all) files created by bwa, or one of them
+        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"),
     output:
-        "mapped/{sample}.bam"
+        "mapped/{sample}.bam",
     log:
-        "logs/bwa_mem2/{sample}.log"
+        "logs/bwa_mem2/{sample}.log",
     params:
-        index="genome.fasta",
         extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
-        sort="none",             # Can be 'none', 'samtools' or 'picard'.
-        sort_order="coordinate", # Can be 'coordinate' (default) or 'queryname'.
-        sort_extra=""            # Extra args for samtools/picard.
+        sort="none",  # Can be 'none', 'samtools' or 'picard'.
+        sort_order="coordinate",  # Can be 'coordinate' (default) or 'queryname'.
+        sort_extra="",  # Extra args for samtools/picard.
     threads: 8
     wrapper:
         "master/bio/bwa-mem2/mem"

bio/bwa-mem2/mem/test/Snakefile_picard

@@ -1,16 +1,17 @@
 rule bwa_mem2_mem:
     input:
-        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"]
+        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
+        # Index can be a list of (all) files created by bwa, or one of them
+        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"),
     output:
-        "mapped/{sample}.bam"
+        "mapped/{sample}.bam",
     log:
-        "logs/bwa_mem/{sample}.log"
+        "logs/bwa_mem/{sample}.log",
     params:
-        index="genome.fasta",
         extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
-        sort="picard",           # Can be 'none', 'samtools' or 'picard'.
-        sort_order="coordinate", # Can be 'coordinate' (default) or 'queryname'.
-        sort_extra=""            # Extra args for samtools/picard.
+        sort="picard",  # Can be 'none', 'samtools' or 'picard'.
+        sort_order="coordinate",  # Can be 'coordinate' (default) or 'queryname'.
+        sort_extra="",  # Extra args for samtools/picard.
     threads: 8
     wrapper:
         "master/bio/bwa-mem2/mem"

bio/bwa-mem2/mem/test/Snakefile_samtools

@@ -1,16 +1,17 @@
 rule bwa_mem2_mem:
     input:
-        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"]
+        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
+        # Index can be a list of (all) files created by bwa, or one of them
+        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"),
     output:
-        "mapped/{sample}.bam"
+        "mapped/{sample}.bam",
     log:
-        "logs/bwa_mem/{sample}.log"
+        "logs/bwa_mem/{sample}.log",
     params:
-        index="genome.fasta",
         extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
-        sort="samtools",         # Can be 'none', 'samtools' or 'picard'.
-        sort_order="coordinate", # Can be 'coordinate' (default) or 'queryname'.
-        sort_extra=""            # Extra args for samtools/picard.
+        sort="samtools",  # Can be 'none', 'samtools' or 'picard'.
+        sort_order="coordinate",  # Can be 'coordinate' (default) or 'queryname'.
+        sort_extra="",  # Extra args for samtools/picard.
     threads: 8
     wrapper:
         "master/bio/bwa-mem2/mem"

bio/bwa-mem2/mem/wrapper.py

@@ -18,6 +18,12 @@
 sort_order = snakemake.params.get("sort_order", "coordinate")
 sort_extra = snakemake.params.get("sort_extra", "")
 
+index = snakemake.input.get("index", "")
+if isinstance(index, str):
+    index = path.splitext(snakemake.input.idx)[0]
+else:
+    index = path.splitext(snakemake.input.idx[0])[0]
+
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 
 # Check inputs/arguments.
@@ -63,7 +69,7 @@
     "(bwa-mem2 mem"
     " -t {snakemake.threads}"
     " {extra}"
-    " {snakemake.params.index}"
+    " {index}"
     " {snakemake.input.reads}"
     " | " + pipe_cmd + ") {log}"
 )

bio/bwa/aln/test/Snakefile

@@ -1,13 +1,14 @@
 rule bwa_aln:
     input:
-        "reads/{sample}.{pair}.fastq"
+        fastq="reads/{sample}.{pair}.fastq",
+        # Index can be a list of (all) files created by bwa, or one of them
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
-        "sai/{sample}.{pair}.sai"
+        "sai/{sample}.{pair}.sai",
     params:
-        index="genome",
-        extra=""
+        extra="",
     log:
-        "logs/bwa_aln/{sample}.{pair}.log"
+        "logs/bwa_aln/{sample}.{pair}.log",
     threads: 8
     wrapper:
         "master/bio/bwa/aln"

bio/bwa/aln/wrapper.py

@@ -5,18 +5,24 @@
 __email__ = "julianderuiter@gmail.com"
 __license__ = "MIT"
 
-
+from os import path
 from snakemake.shell import shell
 
 
 extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 
+index = snakemake.input.idx
+if isinstance(index, str):
+    index = path.splitext(snakemake.input.idx)[0]
+else:
+    index = path.splitext(snakemake.input.idx[0])[0]
+
 shell(
     "bwa aln"
     " {extra}"
     " -t {snakemake.threads}"
-    " {snakemake.params.index}"
-    " {snakemake.input[0]}"
+    " {index}"
+    " {snakemake.input.fastq}"
     " > {snakemake.output[0]} {log}"
 )

bio/bwa/index/test/Snakefile

@@ -1,16 +1,11 @@
 rule bwa_index:
     input:
-        "{genome}.fasta"
+        "{genome}.fasta",
     output:
-        "{genome}.amb",
-        "{genome}.ann",
-        "{genome}.bwt",
-        "{genome}.pac",
-        "{genome}.sa"
+        idx=multiext("{genome}", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     log:
-        "logs/bwa_index/{genome}.log"
+        "logs/bwa_index/{genome}.log",
     params:
-        prefix="{genome}",
-        algorithm="bwtsw"
+        algorithm="bwtsw",
     wrapper:
-        "master/bio/bwa/index"
+        "master/bio/bwa/index"

bio/bwa/index/wrapper.py

@@ -3,7 +3,7 @@
 __email__ = "patrik.smeds@gmail.com"
 __license__ = "MIT"
 
-from os import path
+from os.path import splitext
 
 from snakemake.shell import shell
 
@@ -16,7 +16,7 @@
     raise ValueError("Only one reference genome can be inputed!")
 
 # Prefix that should be used for the database
-prefix = snakemake.params.get("prefix", "")
+prefix = snakemake.params.get("prefix", splitext(snakemake.output.idx[0])[0])
 
 if len(prefix) > 0:
     prefix = "-p " + prefix

bio/bwa/mem-samblaster/test/Snakefile

@@ -1,15 +1,16 @@
 rule bwa_mem:
     input:
-        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"]
+        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
+        # Index can be a list of (all) files created by bwa, or one of them
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         bam="mapped/{sample}.bam",
-        index="mapped/{sample}.bam.bai"
+        index="mapped/{sample}.bam.bai",
     log:
-        "logs/bwa_mem_sambamba/{sample}.log"
+        "logs/bwa_mem_sambamba/{sample}.log",
     params:
-        index="genome",
         extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
-        sort_extra="" # Extra args for sambamba.
+        sort_extra="",  # Extra args for sambamba.
     threads: 8
     wrapper:
         "master/bio/bwa/mem-samblaster"

bio/bwa/mem-samblaster/wrapper.py

@@ -14,6 +14,12 @@
 sort_extra = snakemake.params.get("sort_extra", "")
 samblaster_extra = snakemake.params.get("samblaster_extra", "")
 
+index = snakemake.input.get("index", "")
+if isinstance(index, str):
+    index = path.splitext(snakemake.input.idx)[0]
+else:
+    index = path.splitext(snakemake.input.idx[0])[0]
+
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 
 # Check inputs/arguments.
@@ -27,7 +33,7 @@
     "(bwa mem"
     " -t {snakemake.threads}"
     " {extra}"
-    " {snakemake.params.index}"
+    " {index}"
     " {snakemake.input.reads}"
     " | samblaster"
     " {samblaster_extra}"

bio/bwa/mem/test/Snakefile

@@ -1,17 +1,17 @@
 rule bwa_mem:
     input:
         reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
+        # Index can be a list of (all) files created by bwa, or one of them
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.bam",
     log:
         "logs/bwa_mem/{sample}.log",
     params:
-        index="genome",
         extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
         sorting="none",  # Can be 'none', 'samtools' or 'picard'.
         sort_order="queryname",  # Can be 'queryname' or 'coordinate'.
         sort_extra="",  # Extra args for samtools/picard.
-        tmp_dir="/tmp/",  # Path to temp dir. (optional)
     threads: 8
     wrapper:
         "master/bio/bwa/mem"

bio/bwa/mem/test/Snakefile_picard

@@ -1,12 +1,13 @@
 rule bwa_mem:
     input:
         reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
+        # Index can be a list of (all) files created by bwa, or one of them
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.bam",
     log:
         "logs/bwa_mem/{sample}.log",
     params:
-        index="genome",
         extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
         sort="picard",  # Can be 'none', 'samtools' or 'picard'.
         sort_order="queryname",  # Can be 'queryname' or 'coordinate'.

bio/bwa/mem/test/Snakefile_samtools

@@ -1,12 +1,13 @@
 rule bwa_mem:
     input:
         reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
+        # Index can be a list of (all) files created by bwa, or one of them
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.bam",
     log:
         "logs/bwa_mem/{sample}.log",
     params:
-        index="genome",
         extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
         sorting="samtools",  # Can be 'none', 'samtools' or 'picard'.
         sort_order="queryname",  # Can be 'queryname' or 'coordinate'.
@@ -20,13 +21,13 @@ rule bwa_mem:
 rule bwa_mem_write_index:
     input:
         reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped_with_index/{sample}.bam",
         "mapped_with_index/{sample}.bam.csi",
     log:
         "logs/bwa_mem/{sample}.log",
     params:
-        index="genome",
         extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
         sorting="samtools",  # Can be 'none', 'samtools' or 'picard'.
         sort_order="coordinate",  # Can be 'queryname' or 'coordinate'.