From 7622abdd745c3f2f6e882e2d6fba5a6ce7c1f812 Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@gmail.com>
Date: Thu, 28 Sep 2023 11:49:09 +0200
Subject: [PATCH] catching quast error

---
 conf/modules.config                          | 18 ++++++++++++++----
 subworkflows/local/fasta_contig_filtering.nf |  4 ++--
 2 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 5e616530..dcf825b5 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -134,15 +134,25 @@ process {
         ]
     }
 
-
-    withName: ".*:UNPACK_DB.*" {
+    if (params.kaiju_db || params.kraken2_db || params.checkv_db || params.blast_db) {
+        withName: ".*:UNPACK_DB.*:GUNZIP" {
             publishDir = [
                 path: { "${params.outdir}/databases/" },
                 mode: params.publish_dir_mode,
                 enabled: params.save_databases
             ]
+        }
+
+        withName: ".*:UNPACK_DB.*:UNTAR" {
+                publishDir = [
+                    path: { "${params.outdir}/databases/" },
+                    mode: params.publish_dir_mode,
+                    enabled: params.save_databases
+                ]
+        }
     }
 
+
     //
     // Taxonomic classification
     //
@@ -219,7 +229,7 @@ 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 = { task.exitStatus in [1,2] ? 'ignore' : 'retry' }  // can fail with very few reads
             ext.args      = "--min_contig_length ${params.min_contig_size} --NO_SEQTK"
             publishDir = [
                 path: { "${params.outdir}/assembly/assemblers/trinity/" },
@@ -905,7 +915,7 @@ process {
 
         withName: QUAST {
             ext.args      = "--min-contig 0"
-            errorStrategy = { task.exitStatus == 4 ? 'ignore' : 'terminate' } // can fail if no contigs are present
+            errorStrategy = { task.exitStatus == 4 ? 'ignore' : 'retry' } // can fail if no contigs are present
             publishDir = [
                 path: { "${params.outdir}/consensus_qc/quast/" },
                 mode: params.publish_dir_mode,
diff --git a/subworkflows/local/fasta_contig_filtering.nf b/subworkflows/local/fasta_contig_filtering.nf
index c4f94740..aac73282 100644
--- a/subworkflows/local/fasta_contig_filtering.nf
+++ b/subworkflows/local/fasta_contig_filtering.nf
@@ -7,12 +7,12 @@ include { QUAST  } from '../../modules/nf-core/quast/main'
 // Function to extract the contig size & N' per 100 kbp from the QUAST report
 def getQuastStats(report_file) {
     def contig_size = 0
-    def n_100 = 0
+    def n_100 = 100000 // assume the worst
     report_file.eachLine { line ->
         def contig_size_match = line =~ /Largest contig\s([\d]+)/
         def n_100_match       = line =~ /N's per 100 kbp\s([\d\.]+)/
         if (contig_size_match) contig_size = contig_size_match[0][1].toFloat()
-        if (n_100) n_100 = n_100_match[0][1].toFloat()
+        if (n_100_match) n_100 = n_100_match[0][1].toFloat()
     }
     return [contig_size : contig_size, n_100 : n_100]
 }