feat: explicitly specify bwa index in bwa samxe (#448)

* explicitly specify bwa index in bwa samxe

* Extra docs

* Fixed rest of tests

* Removed misleading comment

bio/bwa/aln/test/Snakefile

@@ -1,7 +1,6 @@
 rule bwa_aln:
     input:
         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",

bio/bwa/mem-samblaster/test/Snakefile

@@ -1,7 +1,6 @@
 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:
         bam="mapped/{sample}.bam",

bio/bwa/mem/test/Snakefile

@@ -1,7 +1,6 @@
 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",

bio/bwa/mem/test/Snakefile_picard

@@ -1,7 +1,6 @@
 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",

bio/bwa/mem/test/Snakefile_samtools

@@ -1,7 +1,6 @@
 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",

bio/bwa/sampe/test/Snakefile

@@ -2,7 +2,6 @@ rule bwa_sampe:
     input:
         fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
         sai=["sai/{sample}.1.sai", "sai/{sample}.2.sai"],
-        # 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",

bio/bwa/sampe/test/Snakefile_picard

@@ -2,7 +2,6 @@ rule bwa_sampe:
     input:
         fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
         sai=["sai/{sample}.1.sai", "sai/{sample}.2.sai"],
-        # 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",

bio/bwa/sampe/test/Snakefile_samtools

@@ -2,7 +2,6 @@ rule bwa_sampe:
     input:
         fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
         sai=["sai/{sample}.1.sai", "sai/{sample}.2.sai"],
-        # 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",

bio/bwa/samse/test/Snakefile

@@ -2,7 +2,6 @@ rule bwa_samse:
     input:
         fastq="reads/{sample}.1.fastq",
         sai="sai/{sample}.1.sai",
-        # 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",

bio/bwa/samse/test/Snakefile_picard

@@ -2,7 +2,6 @@ rule bwa_samse:
     input:
         fastq="reads/{sample}.1.fastq",
         sai="sai/{sample}.1.sai",
-        # 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",

bio/bwa/samse/test/Snakefile_samtools

@@ -2,7 +2,6 @@ rule bwa_samse:
     input:
         fastq="reads/{sample}.1.fastq",
         sai="sai/{sample}.1.sai",
-        # 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",

bio/bwa/samxe/meta.yaml

@@ -1,4 +1,13 @@
 name: "bwa sam(se/pe)"
-description: Map paired-end reads with either bwa samse or sampe. For more information about BWA see `BWA documentation <http://bio-bwa.sourceforge.net/bwa.shtml>`_.
+description: Map paired-end reads with either bwa samse or sampe.
 authors:
   - Filipe G. Vieira
+input:
+  - FASTQ file(s)
+  - SAI file(s)
+  - reference genome
+output:
+  - SAM/BAM alignment file
+notes: |
+  * The `extra` param allows for additional program arguments.
+  * For more information see, http://bio-bwa.sourceforge.net/bwa.shtml

bio/bwa/samxe/test/Snakefile

@@ -2,10 +2,10 @@ rule bwa_sam_pe:
     input:
         fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
         sai=["sai/{sample}.1.sai", "sai/{sample}.2.sai"],
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.pe.sam",
     params:
-        index="genome",
         extra=r"-r '@RG\tID:{sample}\tSM:{sample}'",  # optional: Extra parameters for bwa.
         sort="none",
     log:
@@ -18,10 +18,10 @@ rule bwa_sam_se:
     input:
         fastq="reads/{sample}.1.fastq",
         sai="sai/{sample}.1.sai",
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.se.sam",
     params:
-        index="genome",
         extra=r"-r '@RG\tID:{sample}\tSM:{sample}'",  # optional: Extra parameters for bwa.
         sort="none",
     log:
@@ -34,10 +34,10 @@ rule bwa_bam_pe:
     input:
         fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
         sai=["sai/{sample}.1.sai", "sai/{sample}.2.sai"],
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.pe.bam",
     params:
-        index="genome",
         extra=r"-r '@RG\tID:{sample}\tSM:{sample}'",  # optional: Extra parameters for bwa.
         sort="none",
     log:
@@ -50,10 +50,10 @@ rule bwa_bam_se:
     input:
         fastq="reads/{sample}.1.fastq",
         sai="sai/{sample}.1.sai",
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.se.bam",
     params:
-        index="genome",
         extra=r"-r '@RG\tID:{sample}\tSM:{sample}'",  # optional: Extra parameters for bwa.
         sort="none",
     log:

bio/bwa/samxe/test/Snakefile_picard

@@ -2,10 +2,10 @@ rule bwa_sam_pe:
     input:
         fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
         sai=["sai/{sample}.1.sai", "sai/{sample}.2.sai"],
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.pe.picard_sort.sam",
     params:
-        index="genome",
         extra=r"-r '@RG\tID:{sample}\tSM:{sample}'",  # optional: Extra parameters for bwa.
         sort="picard",  # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'`
         sort_order="queryname",  # optional: Sort by 'queryname' or 'coordinate'
@@ -20,10 +20,10 @@ rule bwa_sam_se:
     input:
         fastq="reads/{sample}.1.fastq",
         sai="sai/{sample}.1.sai",
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.se.picard_sort.sam",
     params:
-        index="genome",
         extra=r"-r '@RG\tID:{sample}\tSM:{sample}'",  # optional: Extra parameters for bwa.
         sort="picard",  # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'`
         sort_order="queryname",  # optional: Sort by 'queryname' or 'coordinate'
@@ -38,10 +38,10 @@ rule bwa_bam_pe:
     input:
         fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
         sai=["sai/{sample}.1.sai", "sai/{sample}.2.sai"],
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.pe.picard_sort.bam",
     params:
-        index="genome",
         extra=r"-r '@RG\tID:{sample}\tSM:{sample}'",  # optional: Extra parameters for bwa.
         sort="picard",  # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'`
         sort_order="queryname",  # optional: Sort by 'queryname' or 'coordinate'
@@ -56,10 +56,10 @@ rule bwa_bam_se:
     input:
         fastq="reads/{sample}.1.fastq",
         sai="sai/{sample}.1.sai",
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.se.picard_sort.bam",
     params:
-        index="genome",
         extra=r"-r '@RG\tID:{sample}\tSM:{sample}'",  # optional: Extra parameters for bwa.
         sort="picard",  # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'`
         sort_order="queryname",  # optional: Sort by 'queryname' or 'coordinate'

bio/bwa/samxe/test/Snakefile_samtools

@@ -2,10 +2,10 @@ rule bwa_sam_pe:
     input:
         fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
         sai=["sai/{sample}.1.sai", "sai/{sample}.2.sai"],
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.pe.samtools_sort.sam",
     params:
-        index="genome",
         extra=r"-r '@RG\tID:{sample}\tSM:{sample}'",  # optional: Extra parameters for bwa.
         sort="samtools",  # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'`
         sort_order="queryname",  # optional: Sort by 'queryname' or 'coordinate'
@@ -20,10 +20,10 @@ rule bwa_sam_se:
     input:
         fastq="reads/{sample}.1.fastq",
         sai="sai/{sample}.1.sai",
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.se.samtools_sort.sam",
     params:
-        index="genome",
         extra=r"-r '@RG\tID:{sample}\tSM:{sample}'",  # optional: Extra parameters for bwa.
         sort="samtools",  # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'`
         sort_order="queryname",  # optional: Sort by 'queryname' or 'coordinate'
@@ -38,10 +38,10 @@ rule bwa_bam_pe:
     input:
         fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
         sai=["sai/{sample}.1.sai", "sai/{sample}.2.sai"],
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.pe.samtools_sort.bam",
     params:
-        index="genome",
         extra=r"-r '@RG\tID:{sample}\tSM:{sample}'",  # optional: Extra parameters for bwa.
         sort="samtools",  # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'`
         sort_order="queryname",  # optional: Sort by 'queryname' or 'coordinate'
@@ -56,10 +56,10 @@ rule bwa_bam_se:
     input:
         fastq="reads/{sample}.1.fastq",
         sai="sai/{sample}.1.sai",
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "mapped/{sample}.se.samtools_sort.bam",
     params:
-        index="genome",
         extra=r"-r '@RG\tID:{sample}\tSM:{sample}'",  # optional: Extra parameters for bwa.
         sort="samtools",  # optional: Enable sorting. Possible values: 'none', 'samtools' or 'picard'`
         sort_order="queryname",  # optional: Sort by 'queryname' or 'coordinate'

bio/bwa/samxe/wrapper.py

@@ -10,6 +10,12 @@
 from snakemake.shell import shell
 
 
+index = snakemake.input.get("idx", "")
+if isinstance(index, str):
+    index = path.splitext(snakemake.input.idx)[0]
+else:
+    index = path.splitext(snakemake.input.idx[0])[0]
+
 # Check inputs.
 fastq = (
     snakemake.input.fastq
@@ -80,7 +86,7 @@
 shell(
     "(bwa {alg}"
     " {extra}"
-    " {snakemake.params.index}"
+    " {index}"
     " {snakemake.input.sai}"
     " {snakemake.input.fastq}"
     " | " + pipe_cmd + ") {log}"