Robust low coverage (#37)

* Handle low-coverage samples

* Fix duplicated sample ID

bin/check_for_empty_assembly.py

@@ -0,0 +1,16 @@
+#!/usr/bin/env python3
+
+import argparse
+import os
+
+def main(args):
+    input_num_bytes = os.path.getsize(args.assembly)
+    if input_num_bytes == 0:
+        with open(args.assembly, 'w') as f:
+            f.write('>1\nN\n')
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--assembly', help='Input assembly to check', required=True)
+    args = parser.parse_args()
+    main(args)

modules/long_read_qc.nf

@@ -80,6 +80,7 @@ process bandage {
     tag { sample_id + ' / ' + assembly_mode }
 
     executor 'local'
+    errorStrategy 'ignore'
 
     publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_bandage.png", mode: 'copy'
 

modules/quast.nf

@@ -20,11 +20,14 @@ process quast {
       printf -- "          value: null\\n"                                                 >> ${sample_id}_${assembler}_${assembly_mode}_quast_provenance.yml
       printf -- "        - parameter: --fast\\n"                                           >> ${sample_id}_${assembler}_${assembly_mode}_quast_provenance.yml
       printf -- "          value: null\\n"                                                 >> ${sample_id}_${assembler}_${assembly_mode}_quast_provenance.yml
+      printf -- "        - parameter: --min-contig\\n"                                     >> ${sample_id}_${assembler}_${assembly_mode}_quast_provenance.yml
+      printf -- "          value: 0\\n"                                                    >> ${sample_id}_${assembler}_${assembly_mode}_quast_provenance.yml
 
       quast \
         --threads ${task.cpus} \
         --space-efficient \
         --fast \
+	--min-contig 0 \
         --output-dir ${sample_id} \
         ${assembly}
 

modules/unicycler.nf

@@ -29,6 +29,7 @@ process unicycler {
 	${long_reads} \
         -o ${sample_id}_assembly
 
+      check_for_empty_assembly.py --assembly ${sample_id}_assembly/assembly.fasta
       sed 's/^>/>${sample_id}_/' ${sample_id}_assembly/assembly.fasta > ${sample_id}_unicycler_${assembly_mode}.fa
       cp ${sample_id}_assembly/assembly.gfa ${sample_id}_unicycler_${assembly_mode}.gfa
       cp ${sample_id}_assembly/unicycler.log ${sample_id}_unicycler_${assembly_mode}.log