From a22e0e4f76b016ac5d29c896ef5004e9d787a555 Mon Sep 17 00:00:00 2001
From: cpauvert <cpauvert@users.noreply.github.com>
Date: Fri, 19 May 2023 17:12:11 +0200
Subject: [PATCH] fix: fallback when plasmids file exists but is empty

---
 workflow/rules/quality_check.smk | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/workflow/rules/quality_check.smk b/workflow/rules/quality_check.smk
index ec8f6e7..c23d6cc 100644
--- a/workflow/rules/quality_check.smk
+++ b/workflow/rules/quality_check.smk
@@ -38,11 +38,14 @@ rule get_contig_list:
         "results/quality_check/{isolate}/{isolate}.genome.fa",
     output:
         "results/quality_check/{isolate}/{isolate}.genome.tsv",
+    log:
+        "logs/quality_check/{isolate}_get_contig_list.log",
     threads: 1
     shell:
         """
-        grep '>' {input} | sed 's/>//' |\
-                awk '{{OFS="\t"; print $0,$0,"contig","linear","-"}}' > {output}
+        (grep '>' {input} | sed 's/>//' |\
+                awk '{{OFS="\t"; print $0,$0,"contig","linear","-"}}' > {output}) \
+        || (cat /dev/null > {output})
         """
 
 
@@ -51,11 +54,14 @@ rule get_plasmid_list:
         "results/plasmid_reconstruction/{isolate}/assembly_graph.cycs.fasta",
     output:
         "results/plasmid_reconstruction/{isolate}/{isolate}.plasmids.tsv",
+    log:
+        "logs/quality_check/{isolate}_get_plasmid_list.log",
     threads: 1
     shell:
         """
-        grep '>' {input} | sed 's/>//' |\
-                awk '{{OFS="\t"; print $0,$0,"plasmid","circular","-"}}' > {output}
+        (grep '>' {input} | sed 's/>//' |\
+                awk '{{OFS="\t"; print $0,$0,"plasmid","circular","-"}}' > {output}) \
+        || (cat /dev/null > {output})
         """
 
 
@@ -65,6 +71,8 @@ rule combine_genome_plasmids:
         "results/plasmid_reconstruction/{isolate}/assembly_graph.cycs.fasta",
     output:
         "results/quality_check/{isolate}/{isolate}.combined.fa",
+    log:
+        "logs/quality_check/{isolate}_combine_genome_plasmids.log",
     threads: 1
     shell:
         "cat {input} > {output}"
@@ -76,6 +84,8 @@ use rule combine_genome_plasmids as create_replicon_list with:
         "results/plasmid_reconstruction/{isolate}/{isolate}.plasmids.tsv",
     output:
         "results/quality_check/{isolate}/{isolate}.combined.tsv",
+    log:
+        "logs/quality_check/{isolate}_create_replicon_list.log",
 
 
 rule checkM_for_quality: