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nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
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DSL2: 'single_end' and 'id_index' not present in meta of BAM input #1040

Closed TCLamnidis closed 3 months ago

TCLamnidis commented 5 months ago

Currently, BAM input channel elements do not have a single_end or an id_index attribute like FASTQ input elements do. Below is a snippet from dumping the bam inpput of the GENOTYPE SWF.

[['id':'JK2802', 'sample_id':'JK2802', 'library_id':'JK2802_SE', 'single_end':true, 'strandedness':'double', 'damage_treatment':'full', 'id_index':'hs37d5_chr21-MT', 'reference':'hs37d5_chr21-MT'], /Users/lamnidis/Software/github/nf-core/eager/work/47/1d8fe5b918f208c6fef2492767e9c1/JK2802_JK2802_SE_hs37d5_chr21-MT_dedupped.bam, /Users/lamnidis/Software/github/nf-core/eager/work/e2/d0468ef91550a2f5dd2e617962aa40/JK2802_JK2802_SE_hs37d5_chr21-MT_dedupped.bam.bai]
[['id':'JK2067', 'sample_id':'JK2067', 'library_id':'JK2067', 'strandedness':'double', 'damage_treatment':'full', 'reference':'hs37d5_chr21-MT'], /Users/lamnidis/Software/github/nf-core/eager/work/43/784d83e3cfc873e4ec4cac35bb7c49/JK2067_JK2067_hs37d5_chr21-MT_dedupped.bam, /Users/lamnidis/Software/github/nf-core/eager/work/64/89df0eeaf04ddc3d97136775474146/JK2067_JK2067_hs37d5_chr21-MT_dedupped.bam.bai]

Should this be added to bam input to make metas consistent?

TCLamnidis commented 3 months ago

This might be fixed in the new template merge #1056 ?

scarlhoff commented 3 months ago

With the new template, the bams will have a "single_end" element and I could add "id_index" by duplicating "reference"

TCLamnidis commented 3 months ago

yes!