Release 2.3 #233
Release 2.3 #233
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Heatmap error, datasources, shorten filenames
Update RNAseq_report.Rmd for DE information
Fix new multiqc
Version changes for release 2.3
Co-authored-by: Till E. <[email protected]>
Add distance info for heatmaps, add heatmap tables, change volcano jitter to points
| mqc_stats <- read.table(file = paste0(wd,"/QC/multiqc_data/multiqc_samtools_stats.txt"), header=TRUE, sep="\t") | ||
| columns <- c( | ||
| "Sample", | ||
| "raw_total_sequences", | ||
| "reads_mapped_percent", | ||
| "reads_duplicated_percent" | ||
| ) | ||
| if (all(columns %in% colnames(mqc_stats))) { | ||
| mqc_version <- 'new_mqc' | ||
| } else { | ||
| stop("Could not find a suitable multiqc table; please provide a correct multiqc.zip file or omit the parameter --multiqc altogether.") | ||
| } |
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That looks like a copy of the code in lines 887-898. Generally it seems not good to have the same code twice, maintenance and so. If possible, might be better to solve that differently.
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I know, this is indeed not a nice code section but unfortunately I have to do this check twice, once inside a nested ifelse and once in a separate ifelse...
Co-authored-by: Daniel Straub <[email protected]>
Fix branch protection bug
second attempt at fixing branch protection -->merging directly as this changes no pipeline code and I need to see if the fix works
third attempt at fixing branch protection
Revert branch.yml changes
Fix path issue with report file
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As https://nfcore.slack.com/archives/CE6SDBX2A/p1663077291333929 and https://nfcore.slack.com/archives/C02AL61NXPH/p1651131006534289 describe the same issue with the failing branch protection, and I could not find any solution there (and my attempts to fix it also failed), I'm going to ignore this error and merge. |
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).