Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Release 2.3 #233

Merged
merged 103 commits into from
Jun 13, 2024
Merged
Changes from 1 commit
Commits
Show all changes
103 commits
Select commit Hold shift + click to select a range
6ca2eab
Changed versions to dev
WackerO Oct 10, 2023
2084b13
Bugfix for nonconformable arrays bug
WackerO Oct 10, 2023
ef825c2
also added padj to hovertext in volcano
WackerO Oct 12, 2023
b735596
Updated changelog
WackerO Oct 13, 2023
63700be
linting
WackerO Oct 13, 2023
ef2f16f
prettier
WackerO Oct 13, 2023
e133651
fixed tests
WackerO Oct 13, 2023
21cfa7c
Bugfix for non-conformable arrays when certain contrasts in a dataset…
WackerO Nov 14, 2023
6d26b45
This should fix the too many devices error
WackerO Feb 5, 2024
9dcd79c
updated changelog
WackerO Feb 5, 2024
58865a8
Replaced double dev.offs with finally
WackerO Feb 12, 2024
84a9b9d
Shortened some output filepaths, added datasources param to make path…
WackerO Feb 15, 2024
c778192
Updated changelog and test profiles
WackerO Feb 20, 2024
d177582
bugfix, docu update
WackerO Feb 20, 2024
803d56a
bugfix
WackerO Feb 20, 2024
6b3199c
file path changes
WackerO Feb 20, 2024
469724b
updated test ymls
WackerO Feb 20, 2024
4a472f8
more yml fixing, pinned validation plugin version
WackerO Feb 20, 2024
6869d81
more yml updates, trying to get rsem to run
WackerO Feb 21, 2024
9655686
Fixed a bug with finally dev.off; restricted rsem pathway analysis to…
WackerO Feb 22, 2024
cf4a195
removed local writes
WackerO Feb 22, 2024
8df1b31
Fixed rsem test
WackerO Feb 27, 2024
db3111c
md5sum update
WackerO Feb 27, 2024
69855ac
changed versions to dev
WackerO Feb 29, 2024
139b7e3
Merge pull request #225 from WackerO/graphics
WackerO Mar 5, 2024
7681ac7
Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…
WackerO Mar 25, 2024
114ecfa
Update RNAseq_report.Rmd
qbicStefanC Mar 26, 2024
63cc932
Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…
WackerO Apr 10, 2024
962c185
fixed version of container, fixed venn path in fulltest
WackerO Apr 10, 2024
c5f0969
struggling with an error
WackerO Apr 11, 2024
00bdd75
Reintroduced changes after finding previous error
WackerO Apr 12, 2024
24b8760
Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…
WackerO Apr 12, 2024
7b24e9c
Added multiqc.zips for the new salmon/rsem output
WackerO Apr 24, 2024
33f01b9
moved heatmap_genelist output to differential analysis results folder
WackerO Apr 24, 2024
582e71f
removed ensembl_id col from pathway heatmaps
WackerO Apr 24, 2024
ebbcf04
fixed plotma issue with empty plots, added clutser param for pathway …
WackerO Apr 25, 2024
5ac6a4f
updated checksums
WackerO Apr 25, 2024
acf798c
Bugfixing
WackerO Apr 28, 2024
0789481
working on removing irrelevant samples from heatmaps_norm
WackerO Apr 29, 2024
b01328b
Undid some changes about sample filtering for heatmaps
WackerO Apr 29, 2024
ce9bf0a
Fixed enrichment plots having their y labels cut off
WackerO Apr 29, 2024
dab8978
Update changelog
WackerO Apr 29, 2024
cb0c1e4
updated test profiles
WackerO Apr 29, 2024
41afb06
fixed multiqc paths in config
WackerO Apr 30, 2024
fb9a4bd
fixed heatmap test path
WackerO Apr 30, 2024
e155229
Merge pull request #226 from WackerO/multiqc_update
WackerO Apr 30, 2024
f1edb41
fixed test profile
WackerO Apr 30, 2024
4f64abd
Merge branch 'dev' into plot_fixes
WackerO Apr 30, 2024
e3a8f66
fixed md5sum
WackerO Apr 30, 2024
920e855
Merge branch 'plot_fixes' of https://github.com/WackerO/rnadeseq into…
WackerO Apr 30, 2024
f7c1ccc
Merge pull request #229 from WackerO/plot_fixes
WackerO May 2, 2024
5e0aacc
Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…
WackerO May 2, 2024
a5725c9
Fixed some things from https://github.com/qbic-pipelines/rnadeseq/pul…
WackerO May 2, 2024
18b6b8a
fixed venn paths
WackerO May 2, 2024
1e366ba
Merge branch 'nonconf_fix' of https://github.com/WackerO/rnadeseq int…
WackerO May 2, 2024
f5b1da2
removed redundant heatmap from test_full.yml
WackerO May 3, 2024
545faee
Merge pull request #221 from WackerO/nonconf_fix
WackerO May 3, 2024
dbefe1b
Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…
WackerO May 3, 2024
6313e20
Merge pull request #228 from qbic-pipelines/qbicStefanC-patch-1
WackerO May 3, 2024
ded6747
Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…
WackerO May 3, 2024
a1e0a93
Updated Changelog
WackerO May 3, 2024
48d3121
linebreak change to restart the github ci tests
WackerO May 6, 2024
c655b56
Merge pull request #231 from WackerO/sc_fixes
WackerO May 6, 2024
9fdf6da
Changed dev to 2.3 in preparattion of release
WackerO May 7, 2024
82f0fae
Undid permission changes from previous PR
WackerO May 13, 2024
7e0d09b
Merge pull request #234 from WackerO/permissions
WackerO May 13, 2024
d2b920c
Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…
WackerO May 13, 2024
bc2e18a
updated changelog
WackerO May 14, 2024
004c78a
Initial template commit
WackerO May 15, 2024
7b2b0f1
Merge branch 'TEMPLATE' into template_merge
WackerO May 15, 2024
a804c98
Further changes for new template, deleted some files, removed some ol…
WackerO May 16, 2024
1630114
fix linting
WackerO May 16, 2024
b704437
prettier
WackerO May 16, 2024
fa909d7
Removed TODOs, removed nf-validation plugin import, changed 1x nf-cor…
WackerO May 16, 2024
5fa7b29
added lib entry to nf-core.yml to skip error
WackerO May 16, 2024
91d9b3d
removed some unnecessary code
WackerO May 16, 2024
4bee02c
Merge pull request #235 from WackerO/template_merge
WackerO May 16, 2024
7d2419d
Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…
WackerO May 16, 2024
8b93f62
add logic to better check which multiqc version is provided
WackerO May 23, 2024
006c695
Update changelog
WackerO May 28, 2024
2ca778c
Merge pull request #236 from WackerO/fix_new_mqc
WackerO Jun 4, 2024
e74d2d0
Merge branch 'dev' into release_2_3
WackerO Jun 4, 2024
b4ffa12
Merge pull request #232 from WackerO/release_2_3
WackerO Jun 5, 2024
43ff5ae
Working on some more changes that need to be included in the upcoming…
WackerO Jun 7, 2024
e4e53bb
All changes should work now; updated changelog
WackerO Jun 10, 2024
0565bb4
fix changelog
WackerO Jun 10, 2024
0726234
minor fixes for release
WackerO Jun 10, 2024
a9ed0f5
Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…
WackerO Jun 10, 2024
f52a95e
Update assets/RNAseq_report.Rmd
WackerO Jun 10, 2024
f94bd2e
Merge pull request #237 from WackerO/mo_changes
WackerO Jun 11, 2024
a915bdb
Update assets/methods_description_template.yml
WackerO Jun 12, 2024
428df02
Fix branch protection bug
WackerO Jun 12, 2024
bf6fbb9
Merge pull request #238 from WackerO/branchpro
WackerO Jun 12, 2024
5dc13c8
second attempt at fixing branch protection
WackerO Jun 12, 2024
7a82849
Merge pull request #239 from WackerO/dev
WackerO Jun 12, 2024
1b765e0
third attempt at fixing branch protection
WackerO Jun 12, 2024
850bf8f
Merge pull request #240 from WackerO/dev
WackerO Jun 12, 2024
8fd4aca
undid branch.yml changes
WackerO Jun 13, 2024
b579def
prettier
WackerO Jun 13, 2024
03d8038
Merge pull request #241 from WackerO/dev
WackerO Jun 13, 2024
1657692
fixed path issue with report file
WackerO Jun 13, 2024
3863f7b
added two params to nfcore.yml to suppress error
WackerO Jun 13, 2024
acd0dbd
Merge pull request #242 from WackerO/dev
WackerO Jun 13, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Bugfix for non-conformable arrays when certain contrasts in a dataset…
… have no significant results
  • Loading branch information
WackerO committed Nov 14, 2023

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature.
commit 21cfa7caa72458124e5140d9aceff73c92fd9845
13 changes: 13 additions & 0 deletions assets/RNAseq_report.Rmd
Original file line number Diff line number Diff line change
@@ -693,6 +693,7 @@ if (run_rlog){
# rlog transformation
rld <- rlog(cds, blind=FALSE)
rld_names <- merge(x=gene_names, y=assay(rld), by.x = "Ensembl_ID", by.y="row.names")
rld_names <- rld_names[order(rld_names$Ensembl_ID),]
write.table(rld_names, "differential_gene_expression/gene_counts_tables/rlog_transformed_gene_counts.tsv", append = FALSE, quote = FALSE, sep = "\t",eol = "\n", na = "NA", dec = ".", row.names = F, qmethod = c("escape", "double"))

# save table to another variable if pathway analysis
@@ -706,6 +707,7 @@ if (run_rlog){
# vst transformation
vsd <- vst(cds, blind=FALSE, nsub = params$nsub_genes)
vsd_names <- merge(x=gene_names, y=assay(vsd), by.x = "Ensembl_ID", by.y="row.names")
vsd_names <- vsd_names[order(vsd_names$Ensembl_ID),]
write.table(vsd_names, "differential_gene_expression/gene_counts_tables/vst_transformed_gene_counts.tsv", append = FALSE, quote = FALSE, sep = "\t",eol = "\n", na = "NA", dec = ".", row.names = F, qmethod = c("escape", "double"))

# save table to another variable if pathway analysis
@@ -1113,9 +1115,20 @@ A PCA of the batch-effect corrected data is shown below and can be found [here](
if (run_rlog) {
assay(rld) <- limma::removeBatchEffect(assay(rld), rld$batch)
rld_corrected <- rld
out_rld <- as.data.frame(assay(rld_corrected))
out_rld <- out_rld[order(rownames(out_rld)),]
out_rld <- cbind(Ensembl_ID = rownames(out_rld), gene_name = rld_names$gene_name, out_rld[,!names(out_rld) %in% c("gene_name")])

write.table(out_rld, file="differential_gene_expression/gene_counts_tables/rlog_transformed_gene_counts_batchcorrected.tsv", quote=F, sep="\t", row.names=F)
} else {
assay(vsd) <- limma::removeBatchEffect(assay(vsd), vsd$batch)
vsd_corrected <- vsd

out_vsd <- as.data.frame(assay(vsd_corrected))
out_vsd <- out_vsd[order(rownames(out_vsd)),]
out_vsd <- cbind(Ensembl_ID = rownames(out_vsd), gene_name = vsd_names$gene_name, out_vsd[,!names(out_vsd) %in% c("gene_name")])

write.table(out_vsd, file="differential_gene_expression/gene_counts_tables/vst_transformed_gene_counts_batchcorrected.tsv", quote=F, sep="\t", row.names=F)
}
pcaData2 <- plotPCA(if (run_rlog) rld else vsd, intgroup=c("combfactor"), ntop = dim(if (run_rlog) rld else vsd)[1], returnData=TRUE)
percentVar <- round(100*attr(pcaData, "percentVar"))