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NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.
https://www.earthbiogenome.org/
GNU General Public License v3.0
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Make execution report default #113

Closed mahesh-panchal closed 3 months ago

mahesh-panchal commented 3 months ago
gbdias commented 3 months ago

I just updated the repo to the latest version then added your fork as a remote to try the default execution report. I get an error within minutes of execution. I don't think it's related to the profiles_patch though, but since there are so many changes since I last ran the main branch I'm not sure what could it be. Did you get this before @MartinPippel @mahesh-panchal?

Jun-17 09:42:54.867 [main] DEBUG nextflow.Session - Session aborted -- Cause: Missing `fromPath` parameter
Jun-17 09:42:54.947 [main] DEBUG nextflow.cli.Launcher - Operation aborted
nextflow.exception.AbortOperationException: Missing `fromPath` parameter

The command:

# Run Nextflow
nextflow run "$NXF_SCRIPT" \
    -profile uppmax \
    -work-dir "$WORKDIR" \
    -resume \
    -ansi-log false \
    --cache "${STORAGEALLOC}/nobackup/database-cache" \
    --outdir "$RESULTS"

The parameters:

# Mandatory - sample metadata
sample:
  name: 'Tetrastemma melanocephalum'

# Optional - HiFi data if available
hifi:
  - reads: '/proj/snic2021-6-194/BGE_Tetrastemma_melanocephalum_assembly/data/outputs/trim_reads_45378607/tetrastemma_hifi.clipped.bam'

Repo version

(nextflow-env) [guibo205@rackham1 Earth-Biogenome-Project-pilot]$ git status
HEAD detached at mahesh_fork/profiles_patch
nothing to commit, working tree clean
(nextflow-env) [guibo205@rackham1 Earth-Biogenome-Project-pilot]$ git log -1
commit e74a9c32f36d13621f744ea5ed96fdc6ddfc813a (HEAD, mahesh_fork/profiles_patch)
Author: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date:   Fri Jun 14 15:19:42 2024 +0000

    Make execution report default
mahesh-panchal commented 3 months ago

Where are you supplying the params.input? I see no --input or -params-file in your nextflow run command.

gbdias commented 3 months ago

oh right, I deleted it by mistake when removing the execution_report profile parameter. Trying again, thanks!

gbdias commented 3 months ago

Maybe we can merge now then. I'm having a hard time testing it because: (01) long queue time for high mem nodes, (02) failure in processes causes everything else to abort (then back to the queue again...). I think we discussed this before, but it would be nice if all processes are executed unless the required input files are not presents. i.e. Perhaps processes that do not depend on MitoHiFi results should not abort when MitoHiFi fails.

mahesh-panchal commented 3 months ago

I'll work on that when I'm back.