Release v0.8.2 [NEXTFLOW version 20.01.0 & 20.04.1 & 20.07.1]

small update

• updated Dockerfiles with procps as suggested in #89 0cab85f
  • WtP results contain now execution report and execution timeline 0cab85f
• added Citations.bib for easy citation (import this file into your citation program) cdea715
  • contains references of all tools we use
  • stored in results/literature/Citations.bib

Release v0.8.1 [NEXTFLOW version 20.01.0 & 20.04.1]

Small update

• update sourmash version to 3.4.1 and better DB handling (#87)
• Readme update to include the WtP pre-print info

Release v0.8.0 [NEXTFLOW version 20.01.0 & 20.04.1]

• reduced the rate of false-positive phage contigs via improving several result cutoffs #86 #80
  • also some cutoffs can now be modified by the user via params
  • e.g: --dv_filter p-value cut-off [default: 0.9]
  • check --help for more Infos
• added virome mode to vibrant and virsorter #81
  • both modes are executed and clearly labelled as such
  • virome mode (takes more time) can be deactivated via adding --virome
  • we recommend in not deactivating it as you get more information with both methods on
• slurm Executer implementation and more singularity tests #84
  • thanks to @mshamash for testing the WtP code
• heatmap visual now scales correctly with the number of contigs and tools #83
• fixed some blast DB distribution bugs af9099c
• a test profile was included #83
  • just add test to the profile e.g. -profile test,slurm,singularity
  • uses 8 assembly files, takes around ~10h on a 24 threads computer
• fixed bugs of WtP not recognising pre-downloaded databases 87b8c25

Release v0.7.1 [NEXTFLOW version 20.01.0]

• small release tackling to remove a critical issue with vibrant 3ffd535
• fixed #78 display of results from tax. classification
  • shows now ("no match") when no phage was assigned to a contig
• fixed chromomap error 5cb02a4

Release v0.7: checkV, tax, QoL

We improved the analysis results after all the phage contig identification steps. With the chromomap annotation, checkV and the sourmash taxonomy you should get a really good idea about each phage predicted contig.

In Detail:

• checkV implementation on positive phage contigs (#70)
• phage identification or annotation can be skipped (#68)
  • e.g. you only want to generate fancy annotation plots
• updated the readme heavily (#72)
• some fixes towards long read .fastq input (b6056f2)
  • it generates tables etc. but is not optimized
  • We focus on that next release
  • it's working, but too many false positive hits, however, with the annotation data etc. its easy to manually validate what's positive
• sourmash taxonomic classification added to positive contigs (#71)
  • you will know if your phage is similar to a described one

Release v0.6: Phage annotation, Singularity and more

As always run a specific release via nextflow run replikation/What_the_Phage -r v0.6 --help

• implemented annotation and visualization of positive contigs #62 #57
  • hmmscan, prodigal
• length filter is included as fragments below 1500 bp are usually false-positive #59
• singularity was implemented #61
• various bug fixes
• --setup flag to pre-download container (docker/singularity) and databases
• unified params for e.g. --database --cachedir
• improved --help and Readme
• implemented a -profile Executers,Engines (see --help ) to better merge and support various profiles
  • e.g. -profile local,docker or ebi,singularity

First Release v0.5 for nextflow 20.01.0

First release v0.5

• Intended and tested on nextflow 20.01.0
• WtP logo (super important)
• Rolled forward to Nextflow 20.01.0 support
• Complete tool control including databases (deactivating tools stops download too) 5c083b4
• Stability for all 10 tools 07fc275
  • Tool error wont kill the whole process
  • Instead they are removed from the final plot figure
  • can have various reasons (e.g. some tools don't analysis contigs of certain lengths)
• Full raw data support for all tools - don't trust us? check the raw data 2824125
• Fixed virfinder by providing a better R input script to extract results for workflow compatibility 07fc275
• All "positive" contig hits are also provided
• All databases are stored in the current dir and are reused

roadmap to next release is phage annotation and analysis of the "10 tools" results (v1.0)

v0.4

• 10 tools are now available and included
• added a few more lines of codes to be more stable with "strange fasta input files"

v0.3

• added upsetR plot for read screening
• added blastDB via phage reference sequences
  • analysis via metaphinder (both metaphinder are shown in the plot)
  • currently labeled as own database

v0.2

• fixed a critical database issue in ubuntu18 and above