Flye working

nf-core · Mar 18, 2024 · 4bfb20d · 4bfb20d
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diff --git a/CITATIONS.md b/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.

diff --git a/conf/modules.config b/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'

diff --git a/docs/output.md b/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)

diff --git a/modules.json b/modules.json
@@ -8,146 +8,104 @@
                     "bakta/bakta": {
                         "branch": "master",
                         "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bakta/baktadbdownload": {
                         "branch": "master",
                         "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/bakta/baktadbdownload/bakta-baktadbdownload.diff"
                     },
                     "canu": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
-                        "installed_by": [
-                            "fastq_trim_fastp_fastqc",
-                            "modules"
-                        ]
+                        "installed_by": ["fastq_trim_fastp_fastqc", "modules"]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
-                        "installed_by": [
-                            "modules",
-                            "fastq_trim_fastp_fastqc"
-                        ]
+                        "installed_by": ["modules", "fastq_trim_fastp_fastqc"]
                     },
                     "flye": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "miniasm": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "c4e79dd48ab2cedea2d7d525582bea061c241e0f",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "nanoplot": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/nanoplot/nanoplot.diff"
                     },
                     "porechop/porechop": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "prokka": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "quast": {
                         "branch": "master",
                         "git_sha": "344638191a5d6b3526556410819dfcf24e98039e",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "racon": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
                         "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
                         "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             },
@@ -156,12 +114,10 @@
                     "fastq_trim_fastp_fastqc": {
                         "branch": "master",
                         "git_sha": "bd448d5c60454640610681515538be3ec66036e4",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/modules/nf-core/flye/environment.yml b/modules/nf-core/flye/environment.yml
diff --git a/modules/nf-core/flye/main.nf b/modules/nf-core/flye/main.nf