refactor: change filtering for failed samples CDCgov#147

slsevilla · Mar 28, 2024 · f0876a8 · f0876a8
1 parent 320cb64
commit f0876a8
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -43,7 +43,7 @@ process {
             [
                 path: { "${params.outdir}/${meta.id}/file_integrity" },
                 mode: 'copy',
-                pattern: "*{_summary.txt}"
+                pattern: "*{_summary_fairy.txt}"
             ]
         ]
     }

diff --git a/modules/local/fairy_corruption_check.nf b/modules/local/fairy_corruption_check.nf
@@ -9,8 +9,7 @@ process CORRUPTION_CHECK {
     val(busco_val)
 
     output:
-    tuple val(meta), path('*_summary.txt'),                    emit: outcome
-    tuple val(meta), path('*_summary_old.txt'),                emit: outcome_to_edit
+    tuple val(meta), path('*_summary_fairy.txt'),                    emit: outcome
     path('*_summaryline.tsv'),                  optional:true, emit: summary_line
     tuple val(meta), path('*.synopsis'),        optional:true, emit: synopsis
     path("versions.yml"),                                      emit: versions
@@ -37,7 +36,7 @@ process CORRUPTION_CHECK {
     script_version=\$(${ica}fairy_proc.sh -V)
 
     #making a copy of the summary file to pass to READ_COUNT_CHECKS to handle file names being the same
-    cp ${prefix}_summary.txt ${prefix}_summary_old.txt
+    mv ${prefix}_summary.txt ${prefix}_summary_fairy.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/workflows/phoenix.nf b/workflows/phoenix.nf
@@ -127,8 +127,9 @@ workflow PHOENIX_EXTERNAL {
 
         //Combining reads with output of corruption check. By=2 is for getting R1 and R2 results
         //The mapping here is just to get things in the right bracket so we can call var[0]
-        read_stats_ch = INPUT_CHECK.out.reads.join(CORRUPTION_CHECK.out.outcome_to_edit, by: [0,0])
-        .join(CORRUPTION_CHECK.out.outcome.splitCsv(strip:true, by:2).map{meta, fairy_outcome -> [meta, [fairy_outcome[0][0], fairy_outcome[1][0]]]}, by: [0,0])
+        read_stats_ch = INPUT_CHECK.out.reads.join(CORRUPTION_CHECK.out.outcome, by: [0,0])
+            .join(CORRUPTION_CHECK.out.outcome.splitCsv(strip:true, by:2).map{meta, fairy_outcome -> [meta, [fairy_outcome[0][0], fairy_outcome[1][0]]]}, by: [0,0])
+            .filter { it[3].findAll {!it.contains('FAILED')}}
 
         //Get stats on raw reads if the reads aren't corrupted
         GET_RAW_STATS (