Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

pipeline does not work if fastp rule is deactivate #15

Closed
ddesvillechabrol opened this issue May 9, 2022 · 1 comment
Closed

pipeline does not work if fastp rule is deactivate #15

ddesvillechabrol opened this issue May 9, 2022 · 1 comment
Labels
bug Something isn't working

Comments

@ddesvillechabrol
Copy link
Collaborator 

#######################################################
# sofware__choice = ["atropos", "cutadapt", "fastp"]
trimming:
    software_choice: fastp
    do: false

MissingInputException in line 351 of /pasteur/zeus/projets/p02/Biomics/Bioinfo/InProgress/B6766/analysis/rnaseq/rnaseq.rules:
Missing input files for rule sample_rRNA:
D080322_N_CD4_TCR_100_S2/fastp/D080322_N_CD4_TCR_100_S2_R1_.fastp.fastq.gz
@ddesvillechabrol ddesvillechabrol added the bug Something isn't working label May 9, 2022
@cokelaer
Copy link
Contributor

Indeed, syntax error and issues with other trimming tools such as cutadapt and atropos.
All fixed in future PR #31

cokelaer added a commit to cokelaer/rnaseq that referenced this issue Sep 20, 2023
@cokelaer
Fixes sequana#31 and sequana#15
f632cc2
cokelaer added a commit to cokelaer/rnaseq that referenced this issue Sep 26, 2023
@cokelaer
Fixes sequana#31 and sequana#15
091a92c
cokelaer added a commit to cokelaer/rnaseq that referenced this issue Sep 26, 2023
@cokelaer
Fixes sequana#31 and sequana#15
130fe6a
cokelaer added a commit that referenced this issue Sep 26, 2023
@cokelaer
Merge pull request #32 from cokelaer/main
0582af6 
Fixes #31 and #15
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@cokelaer @ddesvillechabrol