Julien

Toil uses `/var/run/user/$UID` if it sees it, whether or not it is actually available to Toil's current session

4

Hi, I noticed that u are using `/var/run/user/$UID` to put locally locks on files. It creates problems on our cluster because the way our session are managed by PAM does...

Hi, if no_proxy is written with blank spaces between comma, it will not be correctly handled. example : `no_proxy='example1.com, example2.com'` In addition, by looking at the code I am not...

Hi, A lot of recipes defined here (macse, factqc for examples) needing only a java runtime environment depends on openjdk conda package that provides the whole java dev kit. This...

Hi, The name collision might cause mistakes when using pipes or some tidyverse functions. In general, I would suggest the use of `.data` and `.env` to be added in style...

Database used here

1

Hi, It is unclear here and in your paper what database you are using at the time you are aligning reads against the reference with bowtie2. Is the following what...

Hi, With default `--min-contig` value (500) I got this error: ``` ERROR! Number of chromosomes in /home/jfouret/Documents/github/nexomis/viral-assembly/work/75/1d032b5ce6668a6180f26c036f888a/s1/quast_corrected_input/s1_spades_r naviral.fa and corresponding file inputs/aln01.bam do not match. Use SAM file obtained by...

Add threads options, why and how

2

Hi, You could easily add an option to control the number of threads. A lots of people use an HPC cluster with job scheduler systems, (SLurm, Nextflow, AWS batch etc...)...