Merge pull request #135 from drpatelh/bwa

Update indices syntax for BWA index and mem modules

software/bwa/index/main.nf

@@ -22,13 +22,14 @@ process BWA_INDEX {
     path fasta
 
     output:
-    path "${fasta}.*"   , emit: index
+    path "bwa"          , emit: index
     path "*.version.txt", emit: version
 
     script:
     def software = getSoftwareName(task.process)
     """
-    bwa index $options.args $fasta
+    mkdir bwa
+    bwa index $options.args $fasta -p bwa/${fasta.baseName}
     echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
     """
 }

software/bwa/mem/main.nf

@@ -21,7 +21,6 @@ process BWA_MEM {
     input:
     tuple val(meta), path(reads)
     path  index
-    path  fasta
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -32,13 +31,15 @@ process BWA_MEM {
     def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     """
+    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
+
     bwa mem \\
         $options.args \\
         $read_group \\
         -t $task.cpus \\
-        $fasta \\
+        \$INDEX \\
         $reads \\
-        | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
+        | samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam -
 
     echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
     """

software/bwa/mem/meta.yml

@@ -51,10 +51,7 @@ input:
     - index:
         type: file
         description: BWA genome index files
-        pattern: "*.{amb,ann,bwt,pac,sa}"
+        pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
-    - fasta:
-        type: file
-        description: Input genome fasta file
 output:
     - bam:
         type: file

tests/software/bwa/index/test.yml

@@ -4,11 +4,11 @@
     - bwa
     - bwa_index
   files:
-    - path: output/bwa/NC_010473.fa.amb
+    - path: output/bwa/bwa/NC_010473.amb
       md5sum: 942a990ae872f1c0b8d72dda2db405d5
-    - path: output/bwa/NC_010473.fa.bwt
+    - path: output/bwa/bwa/NC_010473.bwt
       md5sum: 7301b52e2ecb893d429a49fa692447ae
-    - path: output/bwa/NC_010473.fa.pac
+    - path: output/bwa/bwa/NC_010473.pac
       md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
-    - path: output/bwa/NC_010473.fa.sa
+    - path: output/bwa/bwa/NC_010473.sa
-      md5sum: a47dcc92e750e2f16fbd979b8ff9538e
+      md5sum: a47dcc92e750e2f16fbd979b8ff9538e

tests/software/bwa/mem/main.nf

@@ -15,8 +15,7 @@ workflow test_bwa_mem_single_end {
 
     BWA_MEM (
         input,
-        file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
+        file("${launchDir}/tests/data/index/E_coli/bwa/", checkIfExists: true)
-        file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
     )
 }
 
@@ -32,7 +31,6 @@ workflow test_bwa_mem_paired_end {
 
     BWA_MEM (
         input,
-        file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
+        file("${launchDir}/tests/data/index/E_coli/bwa/", checkIfExists: true)
-        file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
     )
 }

tests/software/bwa/mem/test.yml

@@ -6,7 +6,7 @@
     - bwa_mem_single_end
   files:
     - path: output/bwa/test.bam
-      md5sum: 3ee21210bac387e0335008146e4728bc
+      md5sum: 52e81e5bd523d0b27fe533b21a0d80f5
 
 - name: bwa mem paired-end
   command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
@@ -16,4 +16,4 @@
     - bwa_mem_paired_end
   files:
     - path: output/bwa/test.bam
-      md5sum: 510d8acc6448c07cdacce8e64ec0904c
+      md5sum: 86d82fdb68ed384c656cfc62a253052f