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nf-core

Hello,
Are there any existing modules available to extract read IDs from BAM files? I couldn’t find anything similar among the nf-core modules.
I currently have a custom module that performs this task, but I’d prefer to replace it with an nf-core module if one is available —or contribute my implementation if it would be useful.

I'm not sure if there is, but technically the `samtools view` module could be abused to give you want you need. `ext.args2` could be supplied with a pipe command and you write out the read IDs to a file captured by an optional channel.

Thank you for your reply. I will give it a try

technically possible, but not necessarily a good idea :wink:

Hello <@U016SFULDB8>, can you say more as why it's not a good idea?
Do you think it would be relevant to contribute my implementation to nf-core modules?

the samtools view module emits:
```    tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true
    tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true
    tuple val(meta), path("${prefix}.sam"), emit: sam, optional: true
    tuple val(meta), path("${prefix}.${file_type}.bai"), emit: bai, optional: true
    tuple val(meta), path("${prefix}.${file_type}.csi"), emit: csi, optional: true
    tuple val(meta), path("${prefix}.${file_type}.crai"), emit: crai, optional: true
    tuple val(meta), path("${prefix}.unselected.${file_type}"), emit: unselected, optional: true
    tuple val(meta), path("${prefix}.unselected.${file_type}.{csi,crai}"), emit: unselected_index, optional: true```
so yes, you could write some code that writes e.g. a `foo.crai` file that contains the read names (but is NOT an index), but that would be weird and unintuitive

I also remember too late that we're able to make changes to modules incorporated into pipelines and then use `nf-core modules patch &lt;tool/subtool&gt;` to maintain a diff so the module is updatable, but keeps the changes you make.
E,g. you can do
```nf-core modules install samtools/view
vim modules/nf-core/samtools/view/main.nf # edit the file to include post processing and new output channel
nf-core modules patch samtools/view
git add modules/nf-core/samtools/view/
git commit ...```