Merge pull request #23 from CCBR/filteralign-no-index

refactor: don't run index after samtools view
CCBR · Oct 24, 2023 · 3f41ae3 · 3f41ae3
2 parents 432ebfc + 13455c8
commit 3f41ae3
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Showing 3 changed files with 4 additions and 12 deletions.
diff --git a/modules/CCBR/samtools/filteraligned/main.nf b/modules/CCBR/samtools/filteraligned/main.nf
@@ -12,8 +12,8 @@ process SAMTOOLS_FILTERALIGNED {
         tuple val(meta), path(bam), path(bai)
 
     output:
-        tuple val(meta), path("*.unaligned.bam"), path('*.unaligned.bam.bai'), emit: bam
-        path  "versions.yml"                                                 , emit: versions
+        tuple val(meta), path("*.unaligned.bam"), emit: bam
+        path("versions.yml"),                     emit: versions
 
     when:
         task.ext.when == null || task.ext.when
@@ -28,9 +28,6 @@ process SAMTOOLS_FILTERALIGNED {
       -b \\
       -o ${prefix}.unaligned.bam \\
       ${prefix}.bam
-    samtools index \\
-      -@ ${task.cpus} \\
-      ${prefix}.unaligned.bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -40,6 +37,6 @@ process SAMTOOLS_FILTERALIGNED {
 
     stub:
     """
-    touch ${meta.id}.unaligned.bam ${meta.id}.unaligned.bam.bai versions.yml
+    touch ${meta.id}.unaligned.bam versions.yml
     """
 }
diff --git a/tests/config/test_data_CCBR.config b/tests/config/test_data_CCBR.config
@@ -1,5 +1,5 @@
 params {
-    test_data_base = 'https://raw.githubusercontent.com/CCBR/nf-modules/filter-blacklist-subwf/'
+    test_data_base = 'https://raw.githubusercontent.com/CCBR/nf-modules/main/'
 
     test_data {
         test_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz"

diff --git a/tests/modules/CCBR/samtools/filteraligned/test.yml b/tests/modules/CCBR/samtools/filteraligned/test.yml
@@ -6,8 +6,6 @@
   files:
     - path: output/bwa/test.bam
       md5sum: 33be5394f2873956dcac679d78c7e559
-    - path: output/bwa/test.bam.bai
-      md5sum: 9965a3eaf16130c34ded277653b3811f
     - path: output/bwa/versions.yml
     - path: output/samtools/test.unaligned.bam
       md5sum: 60121474c99a15d030b866f459e83a88
@@ -21,8 +19,6 @@
   files:
     - path: output/bwa/test.bam
       md5sum: 319a128e8959023f52490030b5ee457c
-    - path: output/bwa/test.bam.bai
-      md5sum: 55703b9bdf1b9816853dd5222c31fc2e
     - path: output/bwa/versions.yml
     - path: output/samtools/test.unaligned.bam
       md5sum: 029fb4355a96008d6b30c0dcc0f210cb
@@ -35,7 +31,6 @@
     - samtools
   files:
     - path: output/bwa/test.bam
-    - path: output/bwa/test.bam.bai
     - path: output/bwa/versions.yml
     - path: output/samtools/test.unaligned.bam
     - path: output/samtools/versions.yml