From f0876a8857efee7c05eecefad91cc3ea43ef6bf2 Mon Sep 17 00:00:00 2001
From: slsevilla <slsevilla@gmail.com>
Date: Thu, 28 Mar 2024 21:05:15 +0000
Subject: [PATCH] refactor: change filtering for failed samples #147

---
 conf/modules.config                     | 2 +-
 modules/local/fairy_corruption_check.nf | 5 ++---
 workflows/phoenix.nf                    | 5 +++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 1e91a084..42764e8d 100755
--- 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
index b09c675b..8e0ebb6b 100644
--- 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
index 0815080d..3bfbefff 100644
--- 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 (