Merge pull request #200 from AnnaSyme/polishing-wfs

Added new workflow to polish assembly

workflows/genome-assembly/polish-with-long-reads/.dockstore.yml

@@ -0,0 +1,11 @@
+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /Assembly-polishing-with-long-reads.ga
+  testParameterFiles:
+  - /Assembly-polishing-with-long-reads-tests.yml
+  authors:
+  - name: Anna Syme
+    orcid: 0000-0002-9906-0673

workflows/genome-assembly/polish-with-long-reads/Assembly-polishing-with-long-reads-tests.yml

@@ -0,0 +1,16 @@
+- doc: Test outline for Assembly-polishing-with-long-reads
+  job:
+    Assembly to be polished:
+      class: File
+      path: test-data/assembly.fasta
+      filetype: fasta
+    long reads:
+      class: File
+      path: test-data/long_reads.fastqsanger.gz
+      filetype: fastqsanger.gz
+    'minimap setting (for long reads) ': map-ont
+  outputs:
+    Assembly polished by long reads using Racon:
+      path: test-data/assembly_polished_by_long_reads.fasta
+      compare: sim_size
+      delta_frac: 0.2

workflows/genome-assembly/polish-with-long-reads/CHANGELOG.md

@@ -0,0 +1,9 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1] 2023-07-15
+First release.

workflows/genome-assembly/polish-with-long-reads/README.md

@@ -0,0 +1,30 @@
+# Assembly polishing with Racon workflow
+
+## Inputs
+
+- Sequencing reads in format: fastq, fastq.gz, fastqsanger.gz or fastqsanger
+- Genome assembly to be polished, in fasta format
+
+## What does the workflow do
+
+- After long reads have been assembled into a genome (contigs), this can be polished with the same long reads. 
+- This workflow uses the tool minimap2 to map the long reads back to the assembly, and then uses Racon to make polishes. 
+- This is repeated a further 3 times. 
+
+In more detail:
+
+- minimap2 : long reads are mapped to assembly => overlaps.paf.
+- overaps, long reads, assembly => Racon => polished assembly 1
+- using polished assembly 1 as input; repeat minimap2 + racon => polished assembly 2
+- using polished assembly 2 as input, repeat minimap2 + racon => polished assembly 3
+- using polished assembly 3 as input, repeat minimap2 + racon => polished assembly 4
+
+## Settings
+
+- Run as-is or change parameters at runtime.
+- For the input at "minimap settings for long reads", enter (map-pb) for PacBio reads, (map-hifi) for PacBio HiFi reads, or (map-ont) for Oxford Nanopore reads.
+
+## Outputs
+
+There is one output: the polished assembly in fasta format. 
+