2.3.4

What's Changed

• Add heatmap by @hoelzer in #24

Full Changelog: 2.3.3...2.3.4

2.3.3

What's Changed

• Publish Prokka GFF and not only the FAA file by @hoelzer in #23

Full Changelog: 2.3.2...2.3.3

2.3.2

What's Changed

• Add comparison BLASTP vs. DIAMOND to README by @hoelzer in #18
• typo by @hoelzer in #19
• Update info mssg to include BLASTP vs DIAMOND to inform the user by @hoelzer in #20

Full Changelog: 2.3.1...2.3.2

2.3.1

What's Changed

• Revision by @hoelzer in #17
  • improved warnings when non-default POCP values and not a stable release are used

Full Changelog: 2.3.0...2.3.1

2.3.0

What's Changed

• Adjustments after review comments by @hoelzer in #16
  • improved README
  • added information on DIAMOND vs BLASTP for alignment step
  • warning for adjusting core POCP parameters (e-value, ...)
  • allow usage of BLASTP instead of DIAMOND via --blastp switch (but the default is diamond blastp in --ultra-sensitive mode)

Full Changelog: 2.2.0...2.3.0

2.2.0

What's Changed

• Implement one-vs-all comparisons by @hoelzer in #14

I added the one-vs-all mode now. It is automatically activated when you specify a specific genome (--genome) or protein FASTA (--protein) in addition to the default input --genomes or --proteins. If you do that, the comparisons will only be made between the additional genome/protein FASTA vs all others.

For example:

nextflow pull hoelzer/pocp
nextflow run hoelzer/pocp -r 2.2.0 --genomes 'example/*.fasta' --genome example/Cav_10DC88.fasta -profile local,docker

will give you

❯ cat results/pop-matrix.tsv
ID	Cav_10DC88	Cav_11DC096	Cga_08-1274-3	Cga_12-4358	Ctr_A-HAR-13
Cav_10DC88	100.0	98.9172	96.5928	96.4865	83.171
Cav_11DC096	98.9172	100.0	0.0	0.0	0.0
Cga_08-1274-3	96.5928	0.0	100.0	0.0	0.0
Cga_12-4358	96.4865	0.0	0.0	100.0	0.0
Ctr_A-HAR-13	83.171	0.0	0.0	0.0	100.0

Full Changelog: 2.1.0...2.2.0

Diamond alignments instead of Blast

What's Changed

• Replace blast by diamond by @michoug in #11
• finalize blast-diamond switch by @hoelzer in #12

The blast command was replaced by diamond, which is faster in doing (protein) alignments but yields similar results. For example:

Old Results using blast and v2.0.1:

ID	Cav_10DC88	Cga_08-1274-3	Cmu_Nigg	Cps_6BC	Ctr_D-UW-3-CX
Cav_10DC88	100.0	96.8074	83.3151	90.5553	83.9782
Cga_08-1274-3	96.8074	100.0	83.6313	90.4182	84.2515
Cmu_Nigg	83.3151	83.6313	100.0	82.718	96.3984
Cps_6BC	90.5553	90.4182	82.718	100.0	82.7292
Ctr_D-UW-3-CX	83.9782	84.2515	96.3984	82.7292	100.0

New Results using diamond in blastp mode:

ID	Cav_10DC88	Cga_08-1274-3	Cmu_Nigg	Cps_6BC	Ctr_D-UW-3-CX
Cav_10DC88	100.0	96.7532	82.6586	90.0363	83.6512
Cga_08-1274-3	96.7532	100.0	83.5196	90.0476	84.1402
Cmu_Nigg	82.6586	83.5196	100.0	82.3435	96.2859
Cps_6BC	90.0363	90.0476	82.3435	100.0	82.1962
Ctr_D-UW-3-CX	83.6512	84.1402	96.2859	82.1962	100.0

New Contributors

• @michoug made their first contribution in #11

Full Changelog: 2.0.1...2.1.0

2.0.1

Fix queue size in SLURM

2.0.0

What's Changed

This is a complete re-implementation providing now Nextflow support to run the pipeline. Thus, calculations can be parallelized and the pipeline can be easier installed on different systems. It is also possible now to -resume calculations for large input data sets.

• Nextflow implementation by @hoelzer in #7
• finalize Help by @hoelzer in #8

Full Changelog: 1.1.1...2.0.0

Calculate POCP for 1-vs-all

• added a new parameter to calculate 1-vs-all POCP values instead of all-vs-all (default)
• adjusted Readme
• fixes #2