115 add flye to nf corebacass

CITATIONS.md

@@ -38,6 +38,10 @@
 
   > Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15. PMID: 28298431; PMCID: PMC5411767.
 
+- [Flye](https://pubmed.ncbi.nlm.nih.gov/30936562/)
+
+  > Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. doi: 10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.
+
 - [QUAST](https://pubmed.ncbi.nlm.nih.gov/23422339/)
 
   > Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. doi: 10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806.

conf/modules.config

@@ -71,6 +71,17 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+    withName: 'FLYE' {
+        ext.args = {
+            [ params.flye_args ? "${params.flye_args}" : ''].join(' ').trim()
+        }
+        publishDir = [
+            path: { "${params.outdir}/Flye" },
+            mode: params.publish_dir_mode,
+            pattern: "*.{.fasta.gz,log}",
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
     withName: 'MINIMAP2_ALIGN' {
         ext.args = '-x ava-ont'

docs/output.md

@@ -10,18 +10,21 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-- [Quality trimming and QC](#quality-trimming-and-qc)
-  - [Short Read Trimming](#short-read-trimming)
-  - [Short Read RAW QC](#short-read-raw-qc)
-  - [Long Read Trimming](#long-read-trimming)
-  - [Long Read RAW QC](#long-read-raw-qc)
-- [Taxonomic classification](#taxonomic-classification)
-- [Assembly Output](#assembly-output)
-  - [Polished assemblies](#polished-assemblies)
-- [Assembly QC with QUAST](#assembly-qc-with-quast)
-- [Annotation](#annotation)
-- [Report](#report)
-- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
+- [nf-core/bacass: Output](#nf-corebacass-output)
+  - [Introduction](#introduction)
+  - [Pipeline overview](#pipeline-overview)
+  - [Quality trimming and QC](#quality-trimming-and-qc)
+    - [Short Read Trimming](#short-read-trimming)
+    - [Short Read RAW QC](#short-read-raw-qc)
+    - [Long Read Trimming](#long-read-trimming)
+    - [Long Read RAW QC](#long-read-raw-qc)
+  - [Taxonomic classification](#taxonomic-classification)
+  - [Assembly Output](#assembly-output)
+    - [Polished assemblies](#polished-assemblies)
+  - [Assembly QC with QUAST](#assembly-qc-with-quast)
+  - [Annotation](#annotation)
+  - [Report](#report)
+    - [Pipeline information](#pipeline-information)
 
 ## Quality trimming and QC
 
@@ -121,7 +124,7 @@ Exemplary Kraken2 report screenshot:
 
 ## Assembly Output
 
-Trimmed reads are assembled with [Unicycler](https://github.com/rrwick/Unicycler) in `short` or `hybrid` assembly modes. For long-read assembly, there are also `canu` and `miniasm` available.
+Trimmed reads are assembled with [Unicycler](https://github.com/rrwick/Unicycler) in `short` or `hybrid` assembly modes. For long-read assembly, there are also `canu`, `flye`, `miniasm` available.
 Unicycler is a pipeline on its own, which at least for Illumina reads mainly acts as a frontend to Spades with added polishing steps.
 
 <details markdown="1">
@@ -140,6 +143,12 @@ Check out the [Unicycler documentation](https://github.com/rrwick/Unicycler) for
 
 Check out the [Canu documentation](https://canu.readthedocs.io/en/latest/index.html) for more information on Canu output.
 
+- `Flye/`
+  - `*.fasta.gz`: Final assembly in fasta format
+  - `*.log`: Log file summarizing steps and intermediate results
+
+Check out the [Flye documentation](https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md) for more information on Flye output.
+
 - `Miniasm/`
   - `*.fasta.gz`: Assembly in Fasta format
   - `*_assembly_consensus.fasta.gz`: Consensus assembly in fasta format (polished by Racon)

modules.json

@@ -36,6 +36,11 @@
                         "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
                         "installed_by": ["modules", "fastq_trim_fastp_fastqc"]
                     },
+                    "flye": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",