spsp-tools issueshttps://gitlab.sib.swiss/SPSP/spsp-tools/-/issues2019-12-19T10:13:40+01:00https://gitlab.sib.swiss/SPSP/spsp-tools/-/issues/1FastQC before/after reads trimming2019-12-19T10:13:40+01:00anevesFastQC before/after reads trimming@smoretti : Please run FastQC also before trimming reads (*in addition* to running FastQC after trimming reads).
@dterumal: Please show both FastQC reports (before/after) on the SPSP "My QC Reviews" page.
If possible, complete before Ch...@smoretti : Please run FastQC also before trimming reads (*in addition* to running FastQC after trimming reads).
@dterumal: Please show both FastQC reports (before/after) on the SPSP "My QC Reviews" page.
If possible, complete before Christmas, thank you!Sebastien MorettiSebastien Moretti2019-12-20https://gitlab.sib.swiss/SPSP/spsp-tools/-/issues/2Input parameters of script 00 (QC)2021-01-14T16:04:10+01:00anevesInput parameters of script 00 (QC)Script 00 should take as input parameters the following values:
* single_paired_end = {single; paired}
* library_preparation_kit
provided by the backend (please remove any hard-coding of these variables in script 00).
For the adapters:
...Script 00 should take as input parameters the following values:
* single_paired_end = {single; paired}
* library_preparation_kit
provided by the backend (please remove any hard-coding of these variables in script 00).
For the adapters:
Please download all the adapters from: https://github.com/timflutre/trimmomatic/tree/master/adapters and add the following rules in script 00:
If library_preparation_kit contains "Nextera":
use NexteraPE-PE.fa for adapters.
elseif (library_preparation_kit contains "QIASeq" or "TruSeq") and single_paired_end == "paired":
use TruSeq3-PE-2.fa
elseif (library_preparation_kit contains "QIASeq" or "TruSeq") and single_paired_end == "single":
TruSeq3-SE.fa
else
return error
Merci beaucoupSebastien MorettiSebastien Morettihttps://gitlab.sib.swiss/SPSP/spsp-tools/-/issues/3Process FASTA files in addition to FASTQ files2021-01-08T17:50:10+01:00anevesProcess FASTA files in addition to FASTQ files* Bypasser le script 10 quand on a un fichier FASTA au lieu de FASTQ, et donner un flag « green » à cette souche qui aurait déjà un assembly.
* Bypasser l’essentiel du script 11 quand on a un FASTA au lieu de FASTQ, tout en générant le f...* Bypasser le script 10 quand on a un fichier FASTA au lieu de FASTQ, et donner un flag « green » à cette souche qui aurait déjà un assembly.
* Bypasser l’essentiel du script 11 quand on a un FASTA au lieu de FASTQ, tout en générant le fake MLST file et en déplaçant le FASTA qu’on a déjà dans le dossier attendu pour les scripts suivants 12 et 13.Sebastien MorettiSebastien Morettihttps://gitlab.sib.swiss/SPSP/spsp-tools/-/issues/4Update QC thresholds2021-01-14T16:01:55+01:00anevesUpdate QC thresholdsThe strains are assigned a green/orange/red status at the end of script 10. The thresholds for assigning status are not well defined for SARS-CoV-2, because they are too strict (Tim to provide new thresholds) => we need to update the thr...The strains are assigned a green/orange/red status at the end of script 10. The thresholds for assigning status are not well defined for SARS-CoV-2, because they are too strict (Tim to provide new thresholds) => we need to update the thresholds, which are hard-coded in this file:
https://gitlab.sib.swiss/SPSP/spsp-tools/-/blob/master/pipeline/generate_trimming-cleaning_report.pl
Could you please make a virus-specific script based on "generate_trimming-cleaning_report.pl" that will be called from script 10 (i.e. script 00 with `$CLADE = 'virus'`). I could then update the thresholds in that new file as soon as I get them from Tim, thanks a lot.Sebastien MorettiSebastien Moretti