Closed MarieLataretu closed 2 years ago
what's the status here? still needs some testing?
Yes. I did run
nextflow run poreCov.nf -profile test_fastq,local,singularity --cachedir /data/.../porecov_dev/singularity_images
artic_ncov_wf:artic_medaka
and create_summary_report_wf:plot_coverages
failed. I'm not sure, if this is because I used the container of someone else...
The error log says
[...]
FATAL: while extracting /data/.../porecov_dev/singularity_images/raverjay-fastcov-0.1.3--ba8c8cf6ae19.img: root filesystem extraction failed: extract command failed: WARNING: passwd file doesn't exist in container, not updating
[...]
Write on output file failed because No space left on device
[...]
I'm pulling the containers right now
would say its not enough space on wherever its pulling and building (probably the boot disk)
After thousands of resumes with --max_cores 1 --cores 1
, it finally finished :tada:
No errors, no empty output, and the summary report looks fine to me.
From my side, ready to merge, if want more testing, let me know.
forgot to push this last commit
@MarieLataretu thanks. As it is a "external PR" i don't see a running git action. Can you run these dry run commands listed here to check if everything is alright? you can copy past them they take only a few secs: https://github.com/replikation/poreCov/blob/master/.github/workflows/DryRun.yml
they just ensure that the workflow logic for all inputs are in order.
I moved the log message to https://github.com/MarieLataretu/poreCov/blob/master/poreCov.nf#L332 and https://github.com/MarieLataretu/poreCov/blob/master/poreCov.nf#L358. Should be fine, or?
I run the test with nextflow version 21.04.0, see attached files. Looks fine to me!
test_dry_run_fast5.txt test_dry_run_fast5_2.txt test_dry_run_genome.txt test_dry_run_pass.txt test_dry_run_reads.txt test_dry_run_samples.txt test_help.txt tests.sh.txt
thx @MarieLataretu ! works also fine here, will merge and do a prerelease
not tested yet
fixes #167