PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2022-08-10T15:14:30+02:00https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/54Skip prodigal and use curated annotation2022-08-10T15:14:30+02:00avilaHugoSkip prodigal and use curated annotationDear developers,
I have an extensively cured dataset of annotated genomes, but when I run pathofact with fastas files I lose those annotations. Is there a way to use my annotaions to run the program, such as using a gbk or gff file?
(...Dear developers,
I have an extensively cured dataset of annotated genomes, but when I run pathofact with fastas files I lose those annotations. Is there a way to use my annotaions to run the program, such as using a gbk or gff file?
(quick fix if you are a user like me with the same problem: use blast 100% to find match between Prodigal locus tags and your annotations.)https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/59Input: allow to provide a protein FAA file2022-06-15T15:31:24+02:00Valentina Galatavalentina.galata@uni.luInput: allow to provide a protein FAA fileTo be able to include `PathoFact` into other workflows and to use the already existing annotations, it should be allowed to provide a protein FAA file as input (together with the corresponding contigs FASTA).To be able to include `PathoFact` into other workflows and to use the already existing annotations, it should be allowed to provide a protein FAA file as input (together with the corresponding contigs FASTA).https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/77Feature request: include ARO in output reports2021-09-01T14:13:10+02:00Benjamin WingfieldFeature request: include ARO in output reportsHello,
Thanks for making PathoFact, it's awesome!
I ran into a small problem matching up output reports to the CARD database. Sometimes gene names change over time. It would be easier if we had access to `BEST_ARO_HIT` in the output re...Hello,
Thanks for making PathoFact, it's awesome!
I ran into a small problem matching up output reports to the CARD database. Sometimes gene names change over time. It would be easier if we had access to `BEST_ARO_HIT` in the output reports :smile:
Thanks,
BenLaura DeniesLaura Denieshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/10Snakemake: use && or || to concat CMDs in rules2020-06-08T09:09:24+02:00Valentina Galatavalentina.galata@uni.luSnakemake: use && or || to concat CMDs in rulesIf a rule has multiple CMDs use `&&` or `||` to concatenate them (if appropriate)
```bash
# execute cmd1
# if cmd1 fails execute cmd2 otherwise cmd2 is not executed
cmd1 || cmd2
# execute cmd1
# if cmd1 succeeds execute cmd2 otherwise ...If a rule has multiple CMDs use `&&` or `||` to concatenate them (if appropriate)
```bash
# execute cmd1
# if cmd1 fails execute cmd2 otherwise cmd2 is not executed
cmd1 || cmd2
# execute cmd1
# if cmd1 succeeds execute cmd2 otherwise cmd2 is not executed
cmd1 && cmd2
```https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/42intallation with docker/singularity2020-06-08T08:15:55+02:00soilmicrobiomeintallation with docker/singularityI am excited to use this program. But I work on a HPC which does not allow for conda. Is it possible to have the program available to pull with docker/singularity?
thanksI am excited to use this program. But I work on a HPC which does not allow for conda. Is it possible to have the program available to pull with docker/singularity?
thanks