Merge pull request #12 from CCBR/sort-index

output index from samtools sort
CCBR · Oct 19, 2023 · 4d14377 · 4d14377
2 parents fe697a4 + 48ad268
commit 4d14377
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Showing 4 changed files with 25 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,5 +3,6 @@
 - new modules:
   - bwa/index
   - bwa/mem
+    - also runs samtools sort & outputs index in bai format.
   - cutadapt
   - khmer/uniquekmers
diff --git a/modules/CCBR/bwa/mem/main.nf b/modules/CCBR/bwa/mem/main.nf
@@ -9,8 +9,8 @@ process BWA_MEM {
         tuple val(meta_idx), path(index_files)
 
     output:
-        tuple val(meta), path("*.bam"), emit: bam
-        path  "versions.yml"          , emit: versions
+        tuple val(meta), path("*.bam"), path("*.bai"), emit: bam
+        path  "versions.yml"                         , emit: versions
 
     when:
         task.ext.when == null || task.ext.when
@@ -31,7 +31,9 @@ process BWA_MEM {
       -@ ${task.cpus} \\
       -m 2G \\
       -T \$TMP \\
-      \$TMP/align.bam > ${prefix}.bam
+      --write-index \\
+      -o ${prefix}.bam##idx##${prefix}.bam.bai \\
+      \$TMP/align.bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -42,6 +44,6 @@ process BWA_MEM {
 
     stub:
     """
-    touch ${meta.id}.bam versions.yml
+    touch ${meta.id}.bam ${meta.id}.bam.bai versions.yml
     """
 }
diff --git a/modules/CCBR/bwa/mem/meta.yml b/modules/CCBR/bwa/mem/meta.yml
@@ -37,6 +37,10 @@ output:
       type: file
       description: Output BAM file containing read alignments
       pattern: "*.{bam}"
+  - bai:
+      type: file
+      description: Output BAI index file
+      pattern: "*.{bai}"
   - versions:
       type: file
       description: File containing software versions

diff --git a/tests/modules/CCBR/bwa/mem/test.yml b/tests/modules/CCBR/bwa/mem/test.yml
@@ -15,7 +15,18 @@
     - path: output/bwa/bwa/genome.sa
       md5sum: ab3952cabf026b48cd3eb5bccbb636d1
     - path: output/bwa/test.bam
-      md5sum: fe5a30103b245d81a8d37d6144794f56
+      md5sum: 0f7b7413436295bcd839fec262eabb18
+    - path: output/bwa/test.bam.bai
+    - path: output/bwa/versions.yml
+
+- name: bwa mem test_bwa_mem_single_end stub
+  command: nextflow run ./tests/modules/CCBR/bwa/mem -entry test_bwa_mem_single_end -c ./tests/config/nextflow.config -stub
+  tags:
+    - bwa/mem
+    - bwa
+  files:
+    - path: output/bwa/test.bam
+    - path: output/bwa/test.bam.bai
     - path: output/bwa/versions.yml
 
 - name: bwa mem test_bwa_mem_paired_end
@@ -35,5 +46,6 @@
     - path: output/bwa/bwa/genome.sa
       md5sum: ab3952cabf026b48cd3eb5bccbb636d1
     - path: output/bwa/test.bam
-      md5sum: 06b8e7424d97add946ddb07e55f12962
+      md5sum: ae4a49f2dd6a487d75f99c9d3b42858b
+    - path: output/bwa/test.bam.bai
     - path: output/bwa/versions.yml