Alvaro Gonzalez

That fix did not solve the problem for me. I am running this in OpenShift OKD v4, and got the same `chown /bin: operation not permitted` error. The road to...

So there are two ideas on the table: * Define a PVC that will always be mounted on every task pod. The PVC will have reference/public data and will persists...

OpenShift runs then as a non root user by default, so this should be easy to solve by changing the HELM charts for the kubernetes templates.

Here is what we got for a failed RD workflow: [5BUCPE.log](https://github.com/EMBL-EBI-TSI/TESK/files/4862659/5BUCPE.log) [5BUCPE.json.txt](https://github.com/EMBL-EBI-TSI/TESK/files/4862661/5BUCPE.json.txt) This is just one one of the tasks, I can send all the tasks if needed: [task-84008576-lkn67.log](https://github.com/EMBL-EBI-TSI/TESK/files/4862691/task-84008576-lkn67.log) [task-84008576-outputs-filer-n5zm5.log](https://github.com/EMBL-EBI-TSI/TESK/files/4862692/task-84008576-outputs-filer-n5zm5.log)...

I forgot to mention that the file is indeed uploaded to the FTP server:| ``` [cloud-user@ecp-cla WES-cli]$ lftp vm1976.kaj.pouta.csc.fi lftp [email protected]:~> ls c4 c44bad4a-adce-4aed-a2f9-904b334ab283/ c47f4ac9-0a55-4035-bef0-eb2f2745493e/ lftp [email protected]:~> ls c47f4ac9-0a55-4035-bef0-eb2f2745493e/ drwxr-xr-x...

``` [cloud-user@jlcwl ~]$ sudo grep c47f4ac9-0a55-4035-bef0-eb2f2745493e /var/log/pureftpd.log 195.148.30.238 - input [02/Jul/2020:07:34:42 -0000] "PUT /mnt/data/input/c47f4ac9-0a55-4035-bef0-eb2f2745493e/output_3dc07dbe-ff84-482a-8029-3684bdc77fd4/Mills_and_1000G_gold_standard.indels.b37.vcf" 200 86369975 195.148.30.238 - input [02/Jul/2020:07:35:02 -0000] "PUT /mnt/data/input/c47f4ac9-0a55-4035-bef0-eb2f2745493e/output_fa71aec4-b7da-4cc7-a43f-6e5d6bc013b4/U5c_CCGTCC_L001_R1_001.fastq.gz" 200 487611787 195.148.30.238 - input [02/Jul/2020:07:35:06 -0000]...

I forgot the way to reproduce this is: WES URL: csc-wes.c03.k8s-popup.csc.fi workflow_type = cwl workflow_type_version = v1.0 workflow_url = https://github.com/jarnolaitinen/RD_pipeline/blob/master/workflow.cwl Input {"curl_fastq_urls":{"class":"File","path":"http://195.148.30.67:8000/fastq_files_urls.txt"},"curl_reference_genome_url":{"class":"File","path":"http://195.148.30.67:8000/reference_seq_url.txt"},"curl_known_indels_url":{"class":"File","path":"http://195.148.30.67:8000/known_indels_url.txt"},"curl_known_sites_url":{"class":"File","path":"http://195.148.30.67:8000/known_sites_url.txt"},"readgroup_str":"@RG\\tID:Seq01p\\tSM:Seq01\\tPL:ILLUMINA\\tPI:330","sample_name":"abc1","threads":"10","gqb":[20,25,30,35,40,45,50,70,90,99]}

I copied the inpit files to: ftp://ftp-private.ebi.ac.uk:/upload/RD-files/

I just saw that focal is downgraded, so this PR is more a POC than an actual fix.

Thanks. I will wait for [#248](https://github.com/elixir-cloud-aai/cwl-WES/pull/248) to be merged, so I can rebase and fix the CI.