refactor: fastqc ica handling, filtering CDCgov#147 CDCgov#149

slsevilla · Mar 31, 2024 · 1a6fa53 · 1a6fa53
1 parent 25a2ca6
commit 1a6fa53
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Showing 2 changed files with 10 additions and 11 deletions.
diff --git a/modules/local/fastqc.nf b/modules/local/fastqc.nf
@@ -7,10 +7,6 @@ process FASTQC {
     input:
     tuple val(meta), path(reads), val(fairy_outcome)
 
-    when:
-    //if there are scaffolds left after filtering
-    "${fairy_outcome[3]}" == "PASSED: There are reads in ${meta.id} R1/R2 after trimming."
-
     output:
     tuple val(meta), path("*.html"), emit: html
     tuple val(meta), path("*.zip") , emit: zip

diff --git a/workflows/phoenix.nf b/workflows/phoenix.nf
@@ -174,14 +174,17 @@ workflow PHOENIX_EXTERNAL {
         )
         ch_versions = ch_versions.mix(GET_TRIMD_STATS.out.versions)
 
-        // // combing fastp_trimd information with fairy check of reads to confirm there are reads after filtering
-        // trimd_reads_file_integrity_ch = FASTP_TRIMD.out.reads.join(GET_TRIMD_STATS.out.outcome.splitCsv(strip:true, by:5).map{meta, fairy_outcome -> [meta, [fairy_outcome[0][0], fairy_outcome[1][0], fairy_outcome[2][0], fairy_outcome[3][0], fairy_outcome[4][0]]]}, by: [0,0])
+        // combing fastp_trimd information with fairy check of reads to confirm there are reads after filtering
+        trimd_reads_file_integrity_ch = FASTP_TRIMD.out.reads
+            .join(GET_TRIMD_STATS.out.outcome.splitCsv(strip:true, by:5)
+            .map{meta, fairy_outcome -> [meta, [fairy_outcome[0][0], fairy_outcome[1][0], fairy_outcome[2][0], fairy_outcome[3][0], fairy_outcome[4][0]]]}, by: [0,0])
+            .filter { it[2].findAll {!it.contains('FAILED')}}
 
-        // // Running Fastqc on trimmed reads
-        // FASTQCTRIMD (
-        //     trimd_reads_file_integrity_ch
-        // )
-        // ch_versions = ch_versions.mix(FASTQCTRIMD.out.versions.first())
+        // Running Fastqc on trimmed reads
+        FASTQCTRIMD (
+            trimd_reads_file_integrity_ch
+        )
+        ch_versions = ch_versions.mix(FASTQCTRIMD.out.versions.first())
 
         // // Checking for Contamination in trimmed reads, creating krona plots and best hit files
         // KRAKEN2_TRIMD (