Initial Release Request #14
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…eformated output structure
Updated testing; adding yeast workflow
…t profiles are running
…lit fastq by size to by part
…t profiles are running
merge origin/dev onto upstream/dev, keeping all changes from origin/dev
…setting origin/dev to overwrite upstream/dev on pull request
maxulysse
reviewed
Nov 1, 2023
maxulysse
reviewed
Nov 1, 2023
maxulysse
reviewed
Nov 1, 2023
maxulysse
reviewed
Nov 1, 2023
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I don't think these files should be in the pipeline
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I consulted one of the wet lab members who is more familiar with the biological details -- I'll include his response below.
But, briefly, the yeast strain that makes the 'callingcards' work to begin with is engineered. At the moment, all callingcards experiments would need to use these masks and plasmid sequences (adjusted for the genome build). These are used in the default_yeast profile, which also specifies the ignomes sacCer genome, and allows the yeast workflow to run by only providing the samplesheet. Thus, I think it is reasonable to distribute these along with the workflow.
Here is the more detailed version:
The plasmids used to perform the yeast calling card assay contain sequences from the yeast genome. This allows the plasmids to be selected, propagated, and be generally useful as tools in yeast. However, the Ty5 transposable element used to mark TF-binding can also insert into plasmid-borne sequences (Liu et al, 2020 PMID: 32133534). Because the plasmids carry small sequences from the genome, the number of Ty5 insertions mapped to these sequences could be artificially high, simply because there are more molecular copies of these sequences in the nucleus (one copy of each sequence in the haploid genome and 5-10 copies of each sequence on a low-copy plasmid or 50 -100 copies of each sequence on a 2micron plasmid). This could give a false impression of how well the transcription factor binds these sequences. Also, a collection of 50 barcoded Ty5 plasmids, as well as many of the transcription factor-carrying plasmids have already been cloned and are available to the community. This means someone doing the yeast calling card assay for the first time would likely use these available plasmids if possible, rather than clone their own plasmids. So, I think it is reasonable for the pipeline to include masking these regions as an option.
maxulysse
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the 90° corner looks weird with the 45° ones, can we have just one of these 2 possibilities?
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Is this in reference to the labels, like "Process Reads"? If not, which corners?
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I rounded the label corners that were not rounded in 5fa1c19. it does look better that way. If there were other corners, let me know.
maxulysse
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Nov 1, 2023
maxulysse
reviewed
Nov 1, 2023
maxulysse
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Nov 1, 2023
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| reports: | ||
| multiqc_report.html: | ||
| display: "MultiQC HTML report" | ||
| samplesheet.csv: | ||
| display: "Auto-created samplesheet with collated metadata and FASTQ paths" |
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Can you details the simple files created by the pipeline there?
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resolved (i believe) in b326514. I'm not a tower user -- if you (or someone) wouldn't mind glancing at that, I'd appreciate it.
update conda/quay paths in bwa_aln_to_bam/main.nf Co-authored-by: Maxime U Garcia <[email protected]>
…lesheet, error handling in main and tower output config
merging upstream/dev after making review changes
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Hey! Since the master branch is not completely clean, I will merge this PR and create a new Pseudo PR from the current commit to the first one. |
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This represents the proposed initial release of callingcards