From b789faa34b60cb3ef62c8edc47ad8ddbe2724b56 Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Thu, 28 Sep 2023 10:49:44 +0000
Subject: [PATCH] Catchin trinity errors

---
 conf/modules.config                           |  6 +++-
 .../local/fastq_spades_trinity_megahit.nf     | 31 ++++++++-----------
 2 files changed, 18 insertions(+), 19 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 5e616530..360978bf 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -12,6 +12,7 @@
 
 variant_caller              = params.variant_caller
 intermediate_variant_caller = params.intermediate_variant_caller
+assemblers                  = params.assemblers ? params.assemblers.split(',').collect{ it.trim().toLowerCase() } : []
 
 process {
 
@@ -219,7 +220,10 @@ process {
 
         withName: TRINITY {
             cpus          = { check_max( 12    * task.attempt, 'cpus'   ) } // defeault was 1
-            errorStrategy = { task.exitStatus == 2 ? 'ignore' : 'retry' }  // can fail with very few reads
+            errorStrategy = 
+                'megahit' in assemblers || 'spades' in assemblers ? 
+                { task.exitStatus == 2 ? 'ignore' : 'retry' } : // can fail with very few reads see issue #21
+                {'retry'}  
             ext.args      = "--min_contig_length ${params.min_contig_size} --NO_SEQTK"
             publishDir = [
                 path: { "${params.outdir}/assembly/assemblers/trinity/" },
diff --git a/subworkflows/local/fastq_spades_trinity_megahit.nf b/subworkflows/local/fastq_spades_trinity_megahit.nf
index 419dcb02..d131a26f 100644
--- a/subworkflows/local/fastq_spades_trinity_megahit.nf
+++ b/subworkflows/local/fastq_spades_trinity_megahit.nf
@@ -16,10 +16,7 @@ workflow FASTQ_SPADES_TRINITY_MEGAHIT  {
 
     main:
     ch_versions          = Channel.empty()
-    ch_scaffolds         = reads.map{meta,reads -> [meta]}
-    ch_scaffolds_spades  = Channel.empty()
-    ch_scaffolds_trinity = Channel.empty()
-    ch_scaffolds_megahit = Channel.empty()
+    ch_scaffolds         = Channel.empty()
 
     // SPADES
     if ('spades' in assemblers) {
@@ -31,36 +28,37 @@ workflow FASTQ_SPADES_TRINITY_MEGAHIT  {
             )
 
         ch_versions         = ch_versions.mix(SPADES.out.versions.first())
-        ch_scaffolds_spades = SPADES.out.scaffolds
-        ch_scaffolds        = ch_scaffolds.join(ch_scaffolds_spades,remainder: true)
+        ch_scaffolds        = ch_scaffolds.mix( SPADES.out.scaffolds)
     }
 
     // TRINITY
     if ('trinity' in assemblers) {
         TRINITY(reads)
 
+        TRINITY
+            .out
+            .transcript_fasta
+            .filter{ meta, contigs -> contigs != null } // filter out empty contigs check issue #21
+            .set{ch_scaffolds_trinity}
+
         ch_versions          = ch_versions.mix(TRINITY.out.versions.first())
-        ch_scaffolds_trinity = TRINITY.out.transcript_fasta
-        ch_scaffolds         = ch_scaffolds.join(ch_scaffolds_trinity,remainder: true)
+        ch_scaffolds         = ch_scaffolds.mix(ch_scaffolds_trinity)
     }
 
     // MEGAHIT
     if ('megahit' in assemblers) {
         MEGAHIT(reads)
-
         ch_versions          = ch_versions.mix(MEGAHIT.out.versions.first())
-        ch_scaffolds_megahit = MEGAHIT.out.contigs
-        ch_scaffolds         = ch_scaffolds.join(ch_scaffolds_megahit,remainder: true)
+        ch_scaffolds         = ch_scaffolds.mix(MEGAHIT.out.contigs)
     }
 
     // ch_scaffolds, go from [meta,scaffold1,scaffold2] to [meta,[scaffolds]]
     ch_scaffolds
-        .map{
-            it ->
-            [it[0],it[1..-1]]
-        }
+        .groupTuple()
         .set{ch_scaffolds_combined}
 
+    ch_scaffolds_combined.view()
+
     CAT_CAT(ch_scaffolds_combined)
     ch_versions = CAT_CAT.out.versions.first()
 
@@ -68,9 +66,6 @@ workflow FASTQ_SPADES_TRINITY_MEGAHIT  {
 
     emit:
     scaffolds            = CAT_CAT.out.file_out      // channel: [ val(meta), [ scaffolds] ]
-    scaffolds_spades     = ch_scaffolds_spades       // channel: [ val(meta), [ scaffolds] ]
-    ch_scaffolds_trinity = ch_scaffolds_trinity      // channel: [ val(meta), [ scaffolds] ]
-    ch_scaffolds_megahit = ch_scaffolds_megahit      // channel: [ val(meta), [ scaffolds] ]
 
     versions             = ch_versions               // channel: [ versions.yml ]
     // there are not any MQC files available for spades, trinity and megahit