2.1.2021117.1

This update introduces:

• more universal pair-end file file name retreival

2.0.2021115

This update introduces:

• profiles
  • instead of forcing the end user to link to a config file, there are now profiles to choose from. Also, this workflow no longer need to be downloaded from git first. The new recommended usage is

  nextflow run UPHL-BioNGS/Cecret -profile singularity
  

• nextclade has been updated to use --datasets
• nextalign is now an option for multiple sequence alignment instead of mafft (specify params.relatedness = true and params.msa = 'nextalign')
• Cecret_annotation.nf has been removed. Instead, just put fastas into the main workflow by putting them in the same directory.
• Removed fastq files and instead suggests using https://github.com/CDCgov/datasets-sars-cov-2. The summary files from this dataset are now all that is included in the data subdirectory.
• This is a new version because some of the params have changed and may not be backward compatible
• The default depth is now 100X (up from 10X). This can be adjusted back down to 10X by the end user by specifying params.minimum_depth = 10

1.2.20210930

In this new version:

• iqtree had been upgraded to iqtree2
• fixed bugs in single-end workflow
• improved DAG and kraken2 documentation in readme
• fixed bugs in samtools ampliconclip process
• simplified wget in nextclade process
• added fasta-trim-terminal-ambigs.pl to vadr process

1.0.20210107

This release is the final version until something really groundbreaking happens.

Features added :

• the capacity to use fastp instead of seqyclean of read cleaning.
• summary file appears even when kraken2 option is false
• bwa and ivar versions are now in the summary file

Features removed : bcftools (because downloading the container kept failing)

1.1.20210815

Minor but required update to keep compatibility.

Updated VADR processes Cecret.nf and Cecret_annotation.nf

Updated NextClade processes for Cecret.nf and Cecret_annotation.nf
Also, corresponding NextClade paramater was added :

params.nextclade_genes = 'E,M,N,ORF1a,ORF1b,ORF3a,ORF6,ORF7a,ORF7b,ORF8,ORF9b,S'

1.1.20210611

Minor release :

Changes in summary file

• added pangolin_scorpio column
• changes comma in nextclade clades to semi-colon
• removed process combined_summary because collectFile()

1.0.20210604

Not any major changes:

• fixes error in pangolin results column
• adds samtools depth to count bases covered by 10X according to samtools
• moves samtools plot ampliconstats to true by default
• moves pangolin, vadr, and nextclade to better parallelization
• uses collectFile() to combine results into one file for seqyclean, vadr, pangolin, and nextclade
• conforms example config file to more of a standard format
• removes 'StageInMode' for each process for better ease of configuration

Does not tackles moving from pangolin v2 to v3

1.0.20210209

• Adds BAMSNAP
• Removes need of external scripts for renaming files and changes the required sample file to csv
• Adjusts Pangolin for compatibility

1.0.20210119

New in this release:

• NextClade clade results
• An alternative aligner/mapper : minimap2

Version 1

1.20201215

Update README.md