Merge pull request #699 from maxplanck-ie/dev_ksikora2

DESeq2 minor fixes
maxplanck-ie · Oct 7, 2020 · 515b44c · 515b44c
2 parents 1288303 + 7c7cc2a
commit 515b44c
Show file tree

Hide file tree

Showing 12 changed files with 18 additions and 20 deletions.
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 2.2.3
+  version: 2.3.0
 
 source:
   path: ../

diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -1,11 +1,13 @@
 snakePipes News
 ===============
 
-snakePipes 2.x.y
+snakePipes 2.3.0
 ----------------
 
 * Deprecated mode Gruen in scRNAseq.
 * scRNAseq mode Alevin now outputs spliced/unspliced counts for RNA velocity estimation based on Soneson et al.  2020, bioRxiv https://doi.org/10.1101/2020.03.13.990069 .
+* Fixed "external_gene_name" and "Status" columns in DESeq2 html report.
+* Removed warning when sample names start with a number.
 
 
 snakePipes 2.2.3

diff --git a/docs/content/setting_up.rst b/docs/content/setting_up.rst
@@ -34,7 +34,7 @@ The easiest way to install snakePipes is via our conda channel. The following co
 
 .. code:: bash
 
-    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.2.3
+    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.3.0
 
 This way, the software used within snakePipes do not conflict with the software pre-installed on your terminal or in your python environment.
 

diff --git a/docs/content/workflows/scRNA-seq.rst b/docs/content/workflows/scRNA-seq.rst
@@ -6,7 +6,7 @@ scRNA-seq
 What it does
 ------------
 
-The scRNA-seq pipeline is intended to process UMI-based data, expecting the cell barcode and umi in Read1, and the cDNA sequence in Read2. 
+The scRNA-seq pipeline is intended to process UMI-based data, expecting the cell barcode and umi in Read1, and the cDNA sequence in Read2. The workflow has predefined settings for CelSeq2 and 10x data, but can be extended to custom protocols.
 
 There are currently two analysis modes available:
 - "STARsolo" which uses STAR solo for mapping and quantitation.
@@ -145,6 +145,8 @@ Fraction of read length required to overlap the intron
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 In mode Alevin, the fraction of read length required to overlap the intron in order to be counted as "unspliced" is set to 0.2 (i.e. 20%) by default. This corresponds to 10nt in a 50nt-long read, or to 20nt in a 100nt-long read. The user is encouraged to modify this value as deemed appropriate via the ``--readLengthFrx`` commandline argument.
+In practice, this variable affects the length of the exon sequence flank added to the intron sequence to generate reference sequences for Salmon Alevin. Exon sequence flank length is set to one minus 'readLengthFrx' of read length.
+
 
 
 Output structure

diff --git a/docs/index.rst b/docs/index.rst
@@ -34,7 +34,7 @@ Quick start
 
 .. code:: bash
 
-    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.1.1
+    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.3.0
 
 * You can update snakePipes to the latest version available on conda with:
 

diff --git a/snakePipes/__init__.py b/snakePipes/__init__.py
@@ -1 +1 @@
-__version__ = '2.2.3'
+__version__ = '2.3.0'
diff --git a/snakePipes/shared/rscripts/DESeq2Report.Rmd b/snakePipes/shared/rscripts/DESeq2Report.Rmd
@@ -430,10 +430,10 @@ if(!is.null(searchURL) & outputIsHTML) {
 for(i in which(colnames(res.df) %in% c('pvalue', 'padj'))) res.df[, i] <- format(res.df[, i], scientific = TRUE)
 
 if(outputIsHTML) {
-    datatable(head(res.df, n = nBest), options = list(pagingType='full_numbers', pageLength=10, scrollX='100%'), escape = FALSE, rownames = FALSE) %>% formatRound(which(!colnames(res.df) %in% c('pvalue', 'padj', 'Feature')), digits)
+    datatable(head(res.df, n = nBest), options = list(pagingType='full_numbers', pageLength=10, scrollX='100%'), escape = FALSE, rownames = FALSE) %>% formatRound(which(!colnames(res.df) %in% c('pvalue', 'padj', 'Feature','Status','external_gene_name')), digits)
 } else {
     res.df_top <- head(res.df, n = 20)
-    for(i in which(!colnames(res.df) %in% c('pvalue', 'padj', 'Feature'))) res.df_top[, i] <- round(res.df_top[, i], digits)
+    for(i in which(!colnames(res.df) %in% c('pvalue', 'padj', 'Feature','Status','external_gene_name'))) res.df_top[, i] <- round(res.df_top[, i], digits)
     kable(res.df_top)
 }
 

diff --git a/snakePipes/shared/rscripts/noncoding-DESeq2.R b/snakePipes/shared/rscripts/noncoding-DESeq2.R
@@ -77,12 +77,12 @@ bib <- c(
     DESeq2 = citation('DESeq2'))
 
 write.bibtex(bib, file = 'citations.bib')
-file.copy(paste0(snakemake@scriptdir, "/DESeq2Report.Rmd"), to = 'DESeq2_report_basic.Rmd')
+file.copy(paste0(snakemake@scriptdir, "/DESeq2Report.Rmd"), to = file.path(snakemake@params["outdir"],'DESeq2_report_basic.Rmd'))
 
 ## TODO we need 4 of these...
 outprefix = "DEseq_basic"
 cite_options(citation_format="text", style="html", cite.style="numeric", hyperlink=TRUE)
-render('DESeq2_report_basic.Rmd',
+render(file.path(snakemake@params["outdir"],'DESeq2_report_basic.Rmd'),
        output_file = paste0(snakemake@params["outdir"], "/DESeq2_report_genes.html"),
        output_format = "html_document",
        clean = TRUE,
@@ -95,7 +95,7 @@ render('DESeq2_report_basic.Rmd',
            heatmap_topN = 20,
            geneNamesFile = geneNamesFilePath))
 
-render('DESeq2_report_basic.Rmd',
+render(file.path(snakemake@params["outdir"],'DESeq2_report_basic.Rmd'),
        output_file = paste0(snakemake@params["outdir"], "/DESeq2_report_repeat_name.html"),
        output_format = "html_document",
        clean = TRUE,
@@ -108,7 +108,7 @@ render('DESeq2_report_basic.Rmd',
            heatmap_topN = 20,
            geneNamesFile = geneNamesFilePath))
 
-render('DESeq2_report_basic.Rmd',
+render(file.path(snakemake@params["outdir"],'DESeq2_report_basic.Rmd'),
        output_file = paste0(snakemake@params["outdir"], "/DESeq2_report_repeat_class.html"),
        output_format = "html_document",
        clean = TRUE,
@@ -121,7 +121,7 @@ render('DESeq2_report_basic.Rmd',
            heatmap_topN = 20,
            geneNamesFile = geneNamesFilePath))
 
-render('DESeq2_report_basic.Rmd',
+render(file.path(snakemake@params["outdir"],'DESeq2_report_basic.Rmd'),
        output_file = paste0(snakemake@params["outdir"], "/DESeq2_report_repeat_family.html"),
        output_format = "html_document",
        clean = TRUE,

diff --git a/snakePipes/shared/rules/tecounts.snakefile b/snakePipes/shared/rules/tecounts.snakefile
@@ -196,7 +196,7 @@ if sampleSheet:
         benchmark:
             "{}/.benchmark/DESeq2.featureCounts.benchmark".format(get_outdir("DESeq2",sampleSheet))
         params:
-            outdir = get_outdir("DESeq2", sampleSheet),
+            outdir = os.path.join(outdir, get_outdir("DESeq2", sampleSheet)),
             fdr = 0.05,
         conda: CONDA_RNASEQ_ENV
         script: "../rscripts/noncoding-DESeq2.R"
diff --git a/snakePipes/workflows/mRNA-seq/Snakefile b/snakePipes/workflows/mRNA-seq/Snakefile
@@ -21,8 +21,6 @@ include: os.path.join(workflow.basedir, "internals.snakefile")
 ### include modules of other snakefiles ########################################
 ################################################################################
 
-cf.namesOKinR(samples)
-
 # deeptools cmds
 include: os.path.join(maindir, "shared", "tools" , "deeptools_cmds.snakefile")
 

diff --git a/snakePipes/workflows/noncoding-RNA-seq/Snakefile b/snakePipes/workflows/noncoding-RNA-seq/Snakefile
@@ -53,8 +53,6 @@ include: os.path.join(maindir, "shared", "rules", "tecounts.snakefile")
 ## MultiQC
 include: os.path.join(maindir, "shared", "rules", "multiQC.snakefile")
 
-cf.namesOKinR(samples)
-
 ### conditional/optional rules #################################################
 ################################################################################
 def run_FastQC(fastqc):

diff --git a/snakePipes/workflows/scRNAseq/Snakefile b/snakePipes/workflows/scRNAseq/Snakefile
@@ -51,8 +51,6 @@ include: os.path.join(maindir, "shared", "tools" , "deeptools_cmds.snakefile")
 include: os.path.join(maindir, "shared", "rules", "deepTools_RNA.snakefile")
 include: os.path.join(maindir, "shared", "rules", "multiQC.snakefile")
 
-cf.namesOKinR(samples)
-
 
 ### conditional/optional rules #################################################
 ################################################################################