A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

for some mad reason the hisat2 module was directly referencing `params`. Removed madness, made consistent with STAR: <https://github.com/nf-core/modules/pull/10246>

There are complications though, I'll get back to you :wink:

so for me both seq_platform and seq_center should be coming from the meta map

as we do in the read group in sarek for example

agreed! Also means I need to fix star the same way

If I didn't had the <#C06PHJM0Y3D> release today, I would have done it today

&gt; so for me both seq_platform and seq_center should be coming from the meta map
Yes, that would be sensible. And ideally they would be set via the module, rather using a config...

&gt; And ideally they would be set via the module, rather using a config...
ohh,, this isnt the recommended way?
```withName: STAR_ALIGN {
        ext.args = {
            return "........ --outSAMattrRGline 'ID:${meta.id}' 'SM:${meta.id}' 'LB:${meta.read_group_library}' 'PL:${meta.read_group_platform}' 'PU:${meta.read_group_platform_unit}'"
        }
    }```

<@U0974NYS23Y>, that is indeed the current recommended way

I made another PR for Bowtie2 for consistency with this, basically adding some default read groups behaviour: <https://github.com/nf-core/modules/pull/10253> .

Thanks <@UE6D8290F>! This is just the workflow-level install of the same: <https://github.com/nf-core/rnaseq/pull/1713/changes>

I wanted to allow sample-specific values for the tags to address the linked issue, which is what prompted all this.