Remove extra column from blast output #34
Merged
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This is the change needed for seqkit to successfully filter out contaminated contigs, the issues is described in [https://www.ebi.ac.uk/panda/jira/browse/EMG-7172] and affects both human and host decontamination post-assembly. This implies that as of now, it's like we are not decontaminating at all post-assembly.
Jenny is doing a small benchmark of how many of her assemblies are affected by this.
out of ~1200 assemblies, 238 are contaminated by host. She is currently checking how many are contaminated by human.
My understanding is that Sonia already checked, and the blast score isn't used anywhere in our pipelines. If that is NOT the case, this is what the draft PR is for, otherwise we can already implement it in the pipeline.
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).README.md
is updated (including new tool citations and authors/contributors).