Closed npatel-ah closed 8 months ago
rreggiar
commented
11 months ago I've been so focused on fixing other obvious breakpoints in my use case of this that I just confirmed I am also seeing this occur with the Singularity + Slurm. I have an unrelated issue + PR coming up but I'm going to take a look at this too, not sure I can help but will try since I've been working with this for a bit now.
npatel-ah
commented
11 months ago Thank you much for quick response. I will keep an eye on updates.
rreggiar
commented
11 months ago Seems like this works as intended with test_full
In my production runs I'm also providing explicit paths to local references and indexes....I wonder if that could be causing something
rreggiar
commented
11 months ago I don't have time quite yet for a PR but fixing this is caused by multiple processes trying to access star_index while it isn't being collected in the pipeline. Replacing all process arg instances of start_index with star_index.collect() fixes
nictru
commented
10 months ago Hey everyone, sorry for the late response I think I already fixed this, will have my branch merged ASAP and then we can have a second look
rreggiar
commented
10 months ago Yeah, I've done quite a bit of re-work on this pipeline since I found a lot of issues with channel mix-up preventing completion in addition to this... my fork is going to take a bit to merge into dev though since I prioritized functionality on my compute environment over generalizability. @nictru have you also seen stuff like this? It needs a separate issue and I'll try and get a PR up soon but figure I'd check in here.
nictru
commented
10 months ago I also made some larger changes which are currently on the single-stranded branch (the name might be a bit misleading but it was the first reason to create the branch)
To make communication a bit easier, you could text me in the nf-core slack - just head to the nf-core/circrna channel, you will find me
Description of the bug
Hello,
Thank you for the pipeline. I am having quite trouble fully running the pipeline. I tried it with both Docker and Singularity with both master and dev branches and every time different issues occurs. I am listing the one is key for me to move forward,
In the dev branch
I have 6 samples but after the TRIMGALORE/FASTQ steps, it only runs one sample with STAR 1st pass. After failing with I try to resume the pipeline, somehow the STAR part shows compeletly different sample.
Command used and terminal output
Relevant files
No response
System information
nextflow version 23.04.1 Ubuntu 18.04.6 LTS (GNU/Linux 4.15.0-213-generic x86_64) Container Docker Hardware Local Linux
nf-core/circrna -r dev