From 6c85f786cf92ae8bd9374879372c0ad797372faf Mon Sep 17 00:00:00 2001
From: Igor Trujnara <itrujnara@wp.pl>
Date: Thu, 14 Nov 2024 16:09:01 +0100
Subject: [PATCH] Add module to filter single-id rows in merge_ids

---
 conf/modules.config             |  6 ++++++
 subworkflows/local/merge_ids.nf | 10 ++++++++++
 2 files changed, 16 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index 1850d37..4d60d42 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -215,6 +215,12 @@ process {
         ]
     }
 
+    withName: 'REDUCE_IDMAP' {
+        ext.args = "-F\'\t\'"
+        ext.args2 = "\'NF >= 2\'"
+        ext.prefix = { "${meta.id}_idmap" }
+    }
+
     withName: 'MERGE_CSV' {
         ext.args = '-f 1 --outer-join --na 0'
         publishDir = [
diff --git a/subworkflows/local/merge_ids.nf b/subworkflows/local/merge_ids.nf
index ad13275..88613e6 100644
--- a/subworkflows/local/merge_ids.nf
+++ b/subworkflows/local/merge_ids.nf
@@ -5,6 +5,7 @@ include { GAWK as POSTPROCESS_DIAMOND } from '../../modules/nf-core/gawk/main.nf
 include { GAWK as GROUP_DIAMOND       } from '../../modules/nf-core/gawk/main.nf'
 include { CAT_CAT as MERGE_DIAMOND    } from '../../modules/nf-core/cat/cat/main.nf'
 include { CAT_CAT as MERGE_ALL        } from '../../modules/nf-core/cat/cat/main.nf'
+include { GAWK as REDUCE_IDMAP        } from '../../modules/nf-core/gawk/main.nf'
 
 workflow MERGE_IDS {
     take:
@@ -81,6 +82,15 @@ workflow MERGE_IDS {
 
     ch_id_clusters = ch_id_clusters.mix(MERGE_ALL.out.file_out)
 
+    // Reduce idmap
+    REDUCE_IDMAP (
+        MERGE_ALL.out.file_out,
+        []
+    )
+
+    ch_id_map = REDUCE_IDMAP.out.output
+
     emit:
     ch_id_clusters
+    ch_id_map
 }