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Recently we ran into a situation where input bams were not generated by Tempo and the ID was `s_C_000184_T002_d` but the basename of the bam was `s_C_000184_T002_d___bqsr.bam`, causing failures or rec…
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From @cmeesters:
> the log directive is crucial. There is no rule, using it, no task implementing it. No lookup performed by the participants.
> log is its own directive, not a part of the outpu…
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Hi and hope all is well!
I've caught a bug around the ```name``` attribute in Snakemake rules. Specifically the character ```:``` is not allowed and raises an error, but strangely only when runnin…
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I think we need to revisit our trimming parameters for ThruPlex NGS16S libraries (more an issue for the clampi pipeline than this one). If it's straightforward to do, it might be helpful to preserve t…
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- [ ] % dups tal för varje barcode
- [ ] % aligned tal för varje barcode
- [ ] Gc content tal för varje barcode (upd: plot instead)
- [ ] >= 30x (genome fraction with at least 30x coverage) tal for va…
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In order to take full advantage of MultiQC's aggregation report, it needs to find consistent sample names across various datasets. Thus, whenever possible, MultiQC should be using `element_identifier`…
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It seems that falco doesn't handle reverse-complemented read sequences in mapped BAM files correctly.
Specifically, when flag bit 0x04 of a read is not set (i.e. when the read is mapped), falco shoul…
wm75 updated
2 months ago
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![bismark_mbias-CpG_R1](https://github.com/FelixKrueger/Bismark/assets/66713655/44c3c186-28de-4329-bafb-53805a24d9c0)
![bismark_mbias-CpG_R2](https://github.com/FelixKrueger/Bismark/assets/66713655/c…
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I have MegaQC running in a docker container, since I find it easier to get the right environment, and manage data in that form. However, I would then like to upload my MultiQC data to that docker cont…
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- Leave multiQC plots in multiQC
- [x] create sarek_results.py making sarek_results.html
- add to local html:
- [x] text stats:
-sarek_text_stats.py: add samtools stats alignment scores in per…