Fix hopper config #389

ryanjameskennedy · 2025-01-27T09:22:51Z

Description

##Remove elements in cursive as needed.##

If not self-evident, mention what prompted the change.

Summary of the changes made:

Added when operators to all modules that aren't in bacterial_base.nf
Fixed nextflow.hopper.config re singularity image path
Fixed sccmec version file
Fixed handling of ONT samples re fastqc & postalignqc
Moved all when commands to configs
Update fastqc & sccmec mem settings
Replaced nextflow.dev.config & nextflow.hopper.config with nextflow.cmd.config

Tested on all species

Fix hopper config

8c2d7db

ryanjameskennedy requested a review from a team as a code owner January 27, 2025 09:22

ryanjameskennedy added 14 commits January 27, 2025 11:29

Update fastqc mem

879c99d

Update fastqc mem for all configs

6c865d1

Minor adjustments to formatting of configs

e454c81

Create nextflow.lund.config containing both dev and production profiles

52d2c8c

Rename lund config

c057c71

Update workflow calling system and cmd config

9f68521

Fix when cmds re workflow.profile

078dda0

Move when commands to config

4b4ee04

Update mem for sccmec

4c803fa

Fix sccmec versions file

81eddcb

Rm old cmd configs

1aee122

Update when commands in all configs

b6b5f14

Add when operator to all modules not in bacterial base.nf

b7476b0

Fix handling of ONT samples re fastqc & postalignqc

b0499ab

This was linked to issues Jan 30, 2025

enable fastqc module only for short reads #385

Open

enable post-align-qc only for short reads #386

Open