Refactor --callers into individual --variant_caller / --consensus_caller params for flexibility

.github/workflows/ci.yml

@@ -53,6 +53,8 @@ jobs:
     strategy:
       matrix:
         parameters:
+          - "--consensus_caller ivar"
+          - "--variant_caller bcftools --consensus_caller ivar"
           - "--skip_fastp"
           - "--skip_variants"
           - "--skip_cutadapt"

CHANGELOG.md

@@ -14,6 +14,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * [[#232](https://github.com/nf-core/viralrecon/issues/232)] - Remove duplicate variants called by ARTIC ONT pipeline
 * [[#235](https://github.com/nf-core/viralrecon/issues/235)] - Nextclade version bump
 * [[#244](https://github.com/nf-core/viralrecon/issues/244)] - Fix BCFtools consensus generation and masking
+* [[#245](https://github.com/nf-core/viralrecon/issues/245)] - Mpileup file as output
+* [[#247](https://github.com/nf-core/viralrecon/issues/247)] - Add strand-bias filtering option and codon fix in consecutive positions in ivar tsv conversion to vcf
 
 ### Parameters
 
@@ -23,6 +25,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 |                               | `--nextclade_dataset_name`            |
 |                               | `--nextclade_dataset_reference`       |
 |                               | `--nextclade_dataset_tag`             |
+|                               | `--skip_consensus_plots`              |
+|                               | `--consensus_caller`                  |
+| `--callers`                   | `--variant_caller`                    |
 
 > **NB:** Parameter has been __updated__ if both old and new parameter information is present.
 > **NB:** Parameter has been __added__ if just the new parameter information is present.

README.md

@@ -41,13 +41,13 @@ The SRA download functionality has been removed from the pipeline (`>=2.1`) and
     4. Duplicate read marking ([`picard`](https://broadinstitute.github.io/picard/); *optional*)
     5. Alignment-level QC ([`picard`](https://broadinstitute.github.io/picard/), [`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
     6. Genome-wide and amplicon coverage QC plots ([`mosdepth`](https://github.com/brentp/mosdepth/))
-    7. Choice of multiple variant calling and consensus sequence generation routes ([`iVar variants and consensus`](https://github.com/andersen-lab/ivar); *default for amplicon data* *||* [`BCFTools`](http://samtools.github.io/bcftools/bcftools.html), [`BEDTools`](https://github.com/arq5x/bedtools2/); *default for metagenomics data*)
+    7. Choice of multiple variant callers ([`iVar variants`](https://github.com/andersen-lab/ivar); *default for amplicon data* *||* [`BCFTools`](http://samtools.github.io/bcftools/bcftools.html); *default for metagenomics data*)
         * Variant annotation ([`SnpEff`](http://snpeff.sourceforge.net/SnpEff.html), [`SnpSift`](http://snpeff.sourceforge.net/SnpSift.html))
+        * Individual variant screenshots with annotation tracks ([`ASCIIGenome`](https://asciigenome.readthedocs.io/en/latest/))
+    8. Choice of multiple consensus callers ([`BCFTools`](http://samtools.github.io/bcftools/bcftools.html), [`BEDTools`](https://github.com/arq5x/bedtools2/); *default for both amplicon and metagenomics data* *||* [`iVar consensus`](https://github.com/andersen-lab/ivar))
         * Consensus assessment report ([`QUAST`](http://quast.sourceforge.net/quast))
         * Lineage analysis ([`Pangolin`](https://github.com/cov-lineages/pangolin))
         * Clade assignment, mutation calling and sequence quality checks ([`Nextclade`](https://github.com/nextstrain/nextclade))
-        * Individual variant screenshots with annotation tracks ([`ASCIIGenome`](https://asciigenome.readthedocs.io/en/latest/))
-    8. Intersect variants across callers ([`BCFTools`](http://samtools.github.io/bcftools/bcftools.html))
 6. _De novo_ assembly
     1. Primer trimming ([`Cutadapt`](https://cutadapt.readthedocs.io/en/stable/guide.html); *amplicon data only*)
     2. Choice of multiple assembly tools ([`SPAdes`](http://cab.spbu.ru/software/spades/) *||* [`Unicycler`](https://github.com/rrwick/Unicycler) *||* [`minia`](https://github.com/GATB/minia))
@@ -167,6 +167,7 @@ Many thanks to others who have helped out and contributed along the way too, inc
 | [Aengus Stewart](https://github.com/stewarta)             | [The Francis Crick Institute, UK](https://www.crick.ac.uk/)                           |
 | [Alexander Peltzer](https://github.com/apeltzer)          | [Boehringer Ingelheim, Germany](https://www.boehringer-ingelheim.de/)                 |
 | [Alison Meynert](https://github.com/ameynert)             | [University of Edinburgh, Scotland](https://www.ed.ac.uk/)                            |
+| [Anthony Underwood](https://github.com/antunderwood)      | [Centre for Genomic Pathogen Surveillance](https://www.pathogensurveillance.net)      |
 | [Anton Korobeynikov](https://github.com/asl)              | [Saint Petersburg State University, Russia](https://english.spbu.ru/)                 |
 | [Artem Babaian](https://github.com/ababaian)              | [University of British Columbia, Canada](https://www.ubc.ca/)                         |
 | [Dmitry Meleshko](https://github.com/1dayac)              | [Saint Petersburg State University, Russia](https://english.spbu.ru/)                 |