refactor: filtering strategy bbduk CDCgov#147

slsevilla · Mar 31, 2024 · 5221309 · 5221309
1 parent 47a0c5c
commit 5221309
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diff --git a/modules/local/bbduk.nf b/modules/local/bbduk.nf
@@ -13,10 +13,6 @@ process BBDUK {
     tuple val(meta), path('*.log')     , emit: log
     path "versions.yml"                , emit: versions
 
-    when:
-    //if the files are not corrupt and there are equal number of reads in each file then run bbduk
-    "${fairy_outcome[0]}" == "PASSED: File ${meta.id}_R1 is not corrupt." && "${fairy_outcome[1]}" == "PASSED: File ${meta.id}_R2 is not corrupt." && "${fairy_outcome[2]}" == "PASSED: Read pairs for ${meta.id} are equal."
-
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

diff --git a/workflows/phoenix.nf b/workflows/phoenix.nf
@@ -140,7 +140,10 @@ workflow PHOENIX_EXTERNAL {
         ch_versions = ch_versions.mix(GET_RAW_STATS.out.versions)
 
         // Combining reads with output of corruption check
-        bbduk_ch = INPUT_CHECK.out.reads.join(GET_RAW_STATS.out.outcome.splitCsv(strip:true, by:3).map{meta, fairy_outcome -> [meta, [fairy_outcome[0][0], fairy_outcome[1][0], fairy_outcome[2][0]]]}, by: [0,0])
+        bbduk_ch = INPUT_CHECK.out.reads
+            .join(GET_RAW_STATS.out.outcome.splitCsv(strip:true, by:3)
+            .map{meta, fairy_outcome -> [meta, [fairy_outcome[0][0], fairy_outcome[1][0], fairy_outcome[2][0]]]}, by: [0,0])
+            .filter { it[3].findAll {!it.contains('FAILED')}}
 
         // Remove PhiX reads
         BBDUK (