hi @Laurence Kuhlburger, thanks for the great job developing this pipeline! I am using it for some crispr screening analysis, and I would like to contribute .. I was thinking of adding two features that would help me doing my processing: 1. instead of providing both the library table (csv/tsv) and the relative fasta file for bowtie alignment, I would like to add a module to parse the table and produce the fasta automatically 2. I think it would be useful to have a parameter to inject custom arguments to the cutadapt trimming, in the style of what is currently implemented in the nf-core/rnaseq pipeline (e.g. https://nf-co.re/rnaseq/3.14.0/parameters/#extra_trimgalore_args) do you think these features could be useful?

hey Matteo, yes I think that would be great ideas! For n.1 I think i had played around with doing it with groovy in the main.nf crisprseq so it should definitely be doable. Out of curiosity, have you ever run the data with bowtie alignment and gotten data out of it? I have a gut feeling there's a bug somewhere but never found anything yet.

I have done it recently, but I stopped at the quantification because right now I am just doing some preliminary quality control on the libraries and I do not have all the samples required to to the differential test, so basically I have run the trimming with cutadapt, alignment with bowtie and quantification with mageck. there is a bug in the bowtie process call because the input/output does not match the latest version of the module, but this has been already fixed in the development version. Apart from this, and apart my customization of the cutadapt command line (which I think is experiment-dependent), it works

Ah i wasn't aware it was fixed in the dev branch, then it might be good to push for a new release soon

that would be an honor 😄 however, it is something that I never did... is this https://nf-co.re/docs/checklists/pipeline_release the checklist to follow?

yes 🙂 we have 2 small PRs (including yours) + a template update for this release so i think it would be a nice one to do as a first one 😄

hi, I think that the last couple of PRs are merged, now the tests are running on dev... I will work on the new release beginning next week, if it is ok. However, I am reading the guidelines now, and I had a somewhat stupid question... ideas for the next release name 😉 ? I get that the structure is something like spice + female scientist/philosopher, correct?

yes female scientist and a chips flavour 😄