Merge branch 'dev' of https://github.com/Joon-Klaps/viralgenie into dev

Joon-Klaps · Sep 28, 2023 · 12d2274 · 12d2274
2 parents 39dbcef + 9a594c0
commit 12d2274
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Showing 2 changed files with 12 additions and 2 deletions.
diff --git 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 {
 
@@ -229,7 +230,10 @@ process {
 
         withName: TRINITY {
             cpus          = { check_max( 12    * task.attempt, 'cpus'   ) } // defeault was 1
-            errorStrategy = { task.exitStatus in [1,2] ? '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
@@ -35,8 +35,14 @@ workflow FASTQ_SPADES_TRINITY_MEGAHIT  {
     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         = ch_scaffolds.mix(TRINITY.out.transcript_fasta)
+        ch_scaffolds         = ch_scaffolds.mix(ch_scaffolds_trinity)
     }
 
     // MEGAHIT