Merge pull request #6 from BCCDC-PHL/unicycler-circularization-tag

Add support for unicycler-style circularization tags

README.md

@@ -56,6 +56,33 @@ sample-02,/path/to/sample-02_R1.fastq.gz,/path/to/sample-02_R2.fastq.gz,/path/to
 sample-03,/path/to/sample-03_R1.fastq.gz,/path/to/sample-03_R2.fastq.gz,/path/to/sample-03_RL.fastq.gz
 ```
 
+By default, dragonflye will tag circularized contigs with a `circular=Y` annotation in the fasta header, and `circular=N` for linear contigs. For example:
+
+```
+>contig00001 len=5202987 cov=191.0 origname=contig_1_polypolish polish=racon:1 round(s);polypolish:short_reads,1 round(s); sw=dragonflye-flye/1.1.0 date=20230912 circular=Y
+>contig00002 len=3964 cov=155.0 origname=contig_4_polypolish polish=racon:1 round(s);polypolish:short_reads,1 round(s); sw=dragonflye-flye/1.1.0 date=20230912 circular=N
+...
+```
+
+In contrast, [unicycler](https://github.com/rrwick/Unicycler) adds a `circular=true` tag to circularized contigs and no circularization tag to linear contigs. For example:
+
+```
+>1 length=5202987 depth=191.0x circular=true
+>2 length=3964 depth=155.0
+```
+
+Both this pipeline and our [BCCDC-PHL/routine-assembly](https://github.com/BCCDC-PHL/routine-assembly) edit the fasta header to add the sample ID to the front. In addition, this
+pipeline accepts a `--use_unicycler_circularization_tag` flag that will convert `circular=Y` to `circular=true` and will remove `circular=N`.
+
+```
+nextflow run BCCDC-PHL/dragonflye-nf \
+  --hybrid \
+  --use_unicycler_circularization_tag \
+  --fastq_input <short-read fastq input directory> \
+  --fastq_input_long <long-read fastq input directory> \
+  --outdir <output directory>
+```
+
 ## Output
 An output directory will be created for each sample under the directory provided with the `--outdir` flag. The directory will be named by sample ID, inferred from
 the fastq files (all characters before the first underscore in the fastq filenames), or the `ID` field of the samplesheet, if one is used.

modules/dragonflye.nf

@@ -32,6 +32,11 @@ process dragonflye {
         --outdir ${sample_id}_assembly
 
       sed 's/^>/>${sample_id}_/' ${sample_id}_assembly/contigs.fa > ${sample_id}_dragonflye_${assembly_mode}.fa
+      if [ "${params.use_unicycler_circularization_tag}" == "true" ]; then
+        echo 'Switching circularization tags to unicycler-style...' >&2
+	sed -i 's/circular\\=Y/circular\\=true/' ${sample_id}_dragonflye_${assembly_mode}.fa
+	sed -i 's/ circular\\=N//' ${sample_id}_dragonflye_${assembly_mode}.fa
+      fi
       cp ${sample_id}_assembly/flye-unpolished.gfa ${sample_id}_dragonflye_${assembly_mode}_unpolished.gfa
       cp ${sample_id}_assembly/dragonflye.log ${sample_id}_dragonflye_${assembly_mode}.log
       """

nextflow.config

@@ -1,7 +1,7 @@
 manifest {
   author = 'Dan Fornika'
   name = 'BCCDC-PHL/dragonflye-nf'
-  version = '0.1.0'
+  version = '0.1.1'
   description = 'Nextflow wrapper for Dragonflye Assembler'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'
@@ -12,6 +12,7 @@ params {
   bakta = false
   hybrid = false
   long_only = false
+  use_unicycler_circularization_tag = false
   bakta_db = '/data/ref_databases/bakta/latest'
   illumina_suffixes = ['*_R{1,2}_001', '*_R{1,2}', '*_{1,2}' ]
   long_read_suffixes = ['*_RL', '*_L']