refactor: add param for extended_qc CDCgov#151

slsevilla · Apr 1, 2024 · c75a6a9 · c75a6a9
1 parent 5896dcd
commit c75a6a9
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Showing 2 changed files with 15 additions and 12 deletions.
diff --git a/main.nf b/main.nf
@@ -84,6 +84,9 @@ workflow CDC_PHOENIX {
     if (params.input) { ch_input = file(params.input) } else { exit 1, 'For -entry CDC_PHOENIX: Input samplesheet not specified!' }
     ch_versions = Channel.empty() // Used to collect the software versions
 
+    // true is for -entry CDC_PHOENIX and CDC_SCAFFOLDS - used in SPADES
+    extended_qc=false
+
     main:
         PHOENIX_EXQC ( ch_input, ch_versions, true )
 

diff --git a/workflows/phoenix.nf b/workflows/phoenix.nf
@@ -192,18 +192,18 @@ workflow PHOENIX_EXTERNAL {
         )
         ch_versions = ch_versions.mix(KRAKEN2_TRIMD.out.versions)
 
-        // SPADES_WF (
-        //     FASTP_SINGLES.out.reads, \
-        //     FASTP_TRIMD.out.reads, \
-        //     GET_TRIMD_STATS.out.fastp_total_qc, \
-        //     GET_RAW_STATS.out.combined_raw_stats, \
-        //     [], \
-        //     KRAKEN2_TRIMD.out.report, \
-        //     KRAKEN2_TRIMD.out.krona_html, \
-        //     KRAKEN2_TRIMD.out.k2_bh_summary, \
-        //     false
-        // )
-        // ch_versions = ch_versions.mix(SPADES_WF.out.versions)
+        SPADES_WF (
+            FASTP_SINGLES.out.reads, \
+            FASTP_TRIMD.out.reads, \
+            GET_TRIMD_STATS.out.fastp_total_qc, \
+            GET_RAW_STATS.out.combined_raw_stats, \
+            [], \
+            KRAKEN2_TRIMD.out.report, \
+            KRAKEN2_TRIMD.out.krona_html, \
+            KRAKEN2_TRIMD.out.k2_bh_summary, \
+            params.extended_qc
+        )
+        ch_versions = ch_versions.mix(SPADES_WF.out.versions)
 
         // // Rename scaffold headers
         // RENAME_FASTA_HEADERS (