Workaround for CI on assembly

iquasere · Jul 26, 2021 · 5f69b5e · 5f69b5e
1 parent 31f99b2
commit 5f69b5e
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -64,7 +64,7 @@ jobs:
         run: docker run mosca /bin/bash -c "python /share/MOSCA/scripts/preprocess.py -i MOSCA/ci/mt4_R1.fastq,MOSCA/ci/mt4_R2.fastq -t 14 -d mrna -rd resources_directory -n mt_name1 -o output_pp"
 
       - name: Assembly
-        run: docker run mosca /bin/bash -c "python /share/MOSCA/scripts/assembly.py -r MOSCA/ci/mg_R1.fastq,MOSCA/ci/mg_R2.fastq -t 16 -o output_ass"
+        run: docker run mosca /bin/bash -c "python /share/MOSCA/scripts/assembly.py -r MOSCA/ci/mg_R1.fastq,MOSCA/ci/mg_R2.fastq -t 16 -o output_ass --max-ref-number 0"
 
       - name: Annotation
         run: docker run mosca /bin/bash -c "python /share/MOSCA/scripts/annotation.py -i MOSCA/ci/contigs.fasta -t 16 -o output_ann -db MOSCA/ci/ad_uniprot.fasta"
diff --git a/workflow/scripts/assembly.py b/workflow/scripts/assembly.py
@@ -39,6 +39,8 @@ def get_arguments(self):
                             help="Standard deviation of insert size [2500]")
         parser.add_argument("-bq", "--base-qual", type=str, default='phred33', choices=['phred33', 'phred64'],
                             help="Quality format of base call of reads files")
+        parser.add_argument("-mrn", "--max-ref-number", type=int, default=50,
+                            help="Maximum references to be downloaded by MetaQUAST")
 
 
         args = parser.parse_args()
@@ -62,8 +64,9 @@ def percentage_of_reads(self, file):
         lines = handler.readlines()
         return lines[-1].split('%')[0]
 
-    def run_metaquast(self, contigs, out_dir, threads='12'):
-        run_command(f'metaquast.py --threads {threads} --output-dir {out_dir} {contigs}')
+    def run_metaquast(self, contigs, out_dir, threads='12', max_ref_number=50):
+        run_command(f'metaquast.py --threads {threads} --output-dir {out_dir} --max-ref-number {max_ref_number} '
+                    f'{contigs}')
 
     def close_gaps(self, scaffolds, contigs, output_basename, read1, read2, read_length=150, insert_size=1500,
                    std_insert=10, threads=14, base_qual='phred33'):