read length filter before classification #167

[MarieLataretu]

not tested yet

fixes #167

[hoelzer]

what's the status here? still needs some testing?

[MarieLataretu]

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

[replikation]

would say its not enough space on wherever its pulling and building (probably the boot disk)

[MarieLataretu]

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.

[MarieLataretu]

forgot to push this last commit

[replikation]

@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.

[MarieLataretu]

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

[hoelzer]

thx @MarieLataretu ! works also fine here, will merge and do a prerelease