prod-testing

[drernie]

The new pipelines rely on nf-validation and nf-schema, which aren't (easily) accessible during development.
We should add some prod pipelines for post-publication testing, e.g.

• prod-sarek
• prod-fetchngs

These use the publicly released plugin, and perhaps a standard binary of nextflow.

[drernie]

onFilePublish.dest:udp-spec#package=nf-quilt%2fsarek&path=pipeline_info%2fnf_core_sarek_software_mqc_versions.yml <- src:null
ERROR ~ No such file or directory: s3://udp-spec/.quilt/named_packages/nf-quilt/sarek/latest

 -- Check '.nextflow.log' file for details
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:MULTIQC'

Caused by:
  No such file or directory: s3://udp-spec/.quilt/named_packages/nf-quilt/sarek/latest

[drernie]

Non-Fatal error. Probably an nf-prov or nf-schema thing.

NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.9.0/nf-quilt-0.9.0-meta.json NXF_VER=24.10.3 ../nextflow/nextflow run nf-core/sarek -r master -profile test,docker -plugins nf-quilt@0.9.0 --outdir "quilt+s3://udp-spec#package=nf-quilt/sarek"

 N E X T F L O W   ~  version 24.10.3

WARN: =======================================================================
=                                WARNING                                    =
= You are running this script using a un-official plugin repository.        =
=                                                                           =
= https://github.com/quiltdata/nf-quilt/releases/download/0.9.0/nf-quilt-0.9.0-meta.json
=                                                                           =
= This is only meant to be used for plugin testing purposes.                =
=============================================================================

Launching `https://github.com/nf-core/sarek` [admiring_blackwell] DSL2 - revision: ae4dd11acc [master]

onFilePublish.dest:udp-spec#package=nf-quilt%2fsarek&path=pipeline_info%2fexecution_trace_2024-12-24_11-50-38.txt <- src:null
WARN: onFilePublish: no session intialized
`onFlowCreate` nextflow.Session@3d763ae5
ERROR ~ No such file or directory: /var/folders/tz/8q322ht10qzf9pswh01zv6880000gp/T/QuiltPackage18431617393100825025/QuiltPackage.udp_spec_nf_quilt_sarek/pipeline_info/params_2024-12-24_11-50-48.json

 -- Check script '/Users/ernest/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/utils_nfcore_sarek_pipeline/../../nf-core/utils_nextflow_pipeline/main.nf' at line: 80 or see '.nextflow.log' file for more details

[drernie]

Doh. Set default WRITE_BUCKET to something obviously false...

[drernie]

Okay, it works.