Changes according to PR#8

workflow/report/plot_deseq2_FDR_5_perc_MA.rst

-`MA plot <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.plotMA>`_ **(FDR 0.05)**
-shows the log2 fold changes versus the mean of normalized counts from
-`DESeq2 <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf>`_ analysis filtered on a false
-discovery rate (FDR) threshold of 0.05 for pairwise comparisons of samples across the groups from a particular antibody.
-For more information about DESeq2 please see
+The `MA plot <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#ma-plot>`_ **(FDR 0.05)**
+displays the log2 fold changes versus the mean of normalized counts of the
+DESeq2 analysis results.
+The results of this plot are filtered on a false discovery rate (FDR) threshold of 0.05 and represent the comparison of the
+{{snakemake.wildcards["group_1"]}} versus {{snakemake.wildcards["group_2"]}} groups for the
+{{snakemake.wildcards["antibody"]}} antibody. For more information about DESeq2 please see
 `documentation <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_.
 
- 

workflow/report/plot_deseq2_FDR_5_perc_volcano.rst

-**Volcano plot (FDR 0.05)** shows the significance (adjusted p-value) versus the log2 fold changes of the results of the
-`DESeq2 <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf>`_ analysis filtered on a false
-discovery rate (FDR) threshold of 0.05 for pairwise comparisons of samples across the groups from a particular antibody.
-For more information about DESeq2 please see
+**Volcano plot (FDR 0.05)** shows the significance (adjusted p-value) versus the log2 fold changes of the
+DESeq2 analysis results.
+The results of this plot are filtered on a false discovery rate (FDR) threshold of 0.05 and represent the comparison of the
+{{snakemake.wildcards["group_1"]}} versus {{snakemake.wildcards["group_2"]}} groups for the
+{{snakemake.wildcards["antibody"]}} antibody. For more information about DESeq2 please see
 `documentation <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_.

workflow/report/plot_deseq2_heatmap.rst

-`Heatmap plot <https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf>`_ shows for each antibody a heatmap of
-the `rlog <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.rlog>`_ or
+`Heatmap plot <https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf>`_ shows a heatmap of the `rlog <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.rlog>`_ or
 `vst <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.vst>`_ transformed counts from
-DESeq2 analysis. For more information about DESeq2 please see
+DESeq2 analysis for all groups treated with the {{snakemake.wildcards["antibody"]}} antibody
+. For more information about DESeq2 please see
 `documentation <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_.
 

workflow/report/plot_deseq2_pca.rst

@@ -2,5 +2,5 @@
 **(Principal Component Analysis)** describes variance of the
 `rlog <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.rlog>`_ or
 `vst <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.vst>`_ transformed counts from
-DESeq2 analysis with regard to the antibody used. For more information about DESeq2 please see
+DESeq2 analysis with regard to the used {{snakemake.wildcards["antibody"]}} antibody. For more information about DESeq2 please see
 `documentation <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_.

workflow/report/plot_deseq2_sample_corr_heatmap.rst

 Correlation `heatmap plots <https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf>`_ shows heatmaps of the
 `rlog <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.rlog>`_ or
 `vst <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.vst>`_ transformed counts from
-DESeq2 analysis for each pairwise comparison of samples across the groups from a particular antibody. For more information about DESeq2 please
+the DESeq2 analysis. The results of this plot represent the comparison of the
+{{snakemake.wildcards["group_1"]}} versus {{snakemake.wildcards["group_2"]}} groups treated with the
+{{snakemake.wildcards["antibody"]}} antibody. For more information about DESeq2 please
 see `documentation <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_.

workflow/report/plot_deseq2_scatter.rst

 **Scatter plots** uses the matrix of the
 `rlog <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.rlog>`_ or
 `vst <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.vst>`_ transformed counts from
-DESeq2 analysis for pairwise comparisons of samples across the groups from a particular antibody. For more information about DESeq2 please see
-`documentation <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_.
+the DESeq2 analysis. The results of this plot represent the comparison of the
+{{snakemake.wildcards["group_1"]}} versus {{snakemake.wildcards["group_2"]}} groups treated with the
+{{snakemake.wildcards["antibody"]}} antibody. For more information about DESeq2 please
+see `documentation <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_.
+

workflow/report/plot_heatmap_deeptools.rst

 **deepTools** `plotHeatmap <https://deeptools.readthedocs.io/en/develop/content/tools/plotHeatmap.html>`_ creates a
-heatmap for scores over sets of genomic regions and gives a visualisation for the genome-wide enrichment of the samples.
-The `scores <https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html>`_ represent the signal over a
-set of regions where all regions are scaled to the same size.
+heatmap of read coverage over sets of genomic regions and gives a visualisation for the genome-wide enrichment of the samples.

workflow/report/plot_macs2_qc.rst

 `MACS2 <https://github.com/macs3-project/MACS/blob/master/README.md>`_ **callpeak quality control plots** show for all
-samples and their associated controls the number of peaks and their distributions of peak length, fold-change, FDR and
-p-value from the results of the
+samples and their associated controls the number of peaks and their distributions of peak length, the
+`fold-change <https://github.com/macs3-project/MACS/blob/master/docs/callpeak.md#output-files>`_ of
+the enrichment for their peak summit against random Poisson distribution, FDR and p-value from the results of the
 `MACS callpeak analysis <https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html>`_.
 For more information about Model-based Analysis of ChIP-Seq (MACS) please see published
 `article <https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137>`_.

workflow/report/plot_profile_deeptools.rst

 **deepTools** `plotProfile <https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html>`_ creates a
-profile plot for scores over sets of genomic regions and gives a visualisation for the genome-wide enrichment of the
-samples. The `scores <https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html>`_ represent the
-signal over a set of regions where all regions are scaled to the same size.
+profile plot of read coverage over sets of genomic regions and gives a visualisation for the genome-wide enrichment of the
+samples.

workflow/report/plot_quality_by_cycle_picard_mm.rst

 `Mean quality by cycle plot
 <https://gatk.broadinstitute.org/hc/en-us/articles/360040506831-MeanQualityByCycle-Picard->`_ **(Picard)** is used as
 quality control for sequencing machine performance and collects the mean quality by cycle of the bam files after
-filtering, sorting, merging and removing orphans. Any spikes in quality within reads may indicate technical problems
+filtering, sorting, merging and removing orphans. Clear drops in quality within reads may indicate technical problems
 during sequencing. For more information about `collected Picard metrics
 <https://gatk.broadinstitute.org/hc/en-us/articles/360037594031-CollectMultipleMetrics-Picard->`_ please
 see `documentation <https://broadinstitute.github.io/picard/>`_.

workflow/rules/consensus_peak_analysis.smk

@@ -194,39 +194,38 @@ rule featurecounts_deseq2:
         igv_FDR_5_bed="results/IGV/consensus/merged_library.{antibody}.consensus_{peak}-peaks.deseq2.FDR_0.05.igv.txt",
         plot_FDR_1_perc_MA=report(
             directory("results/deseq2/comparison_plots/MA_plots/FDR_0.01_{antibody}consensus_{peak}-peaks"),
-            patterns=["{antibody}.{{group_1_vs_group_2}}.MA-plot_FDR_0.01.pdf"],
+            patterns=["{antibody}.{group_1}_{antibody_1}_{control_1}vs{group_2}_{antibody_2}_{control_2}.MA-plot_FDR_0.01.pdf"],
             caption = "../report/plot_deseq2_FDR_1_perc_MA.rst",
             category = "DESeq2"),
         plot_FDR_5_perc_MA=report(
             directory("results/deseq2/comparison_plots/MA_plots/FDR_0.05_{antibody}consensus_{peak}-peaks"),
-            patterns=["{antibody}.{{group_1_vs_group_2}.MA-plot_FDR_0.05.pdf"],
+            patterns=["{antibody}.{group_1}_{antibody_1}_{control_1}vs{group_2}_{antibody_2}_{control_2}.MA-plot_FDR_0.05.pdf"],
             caption = "../report/plot_deseq2_FDR_5_perc_MA.rst",
             category = "DESeq2"),
         plot_FDR_1_perc_volcano=report(
             directory("results/deseq2/comparison_plots/volcano_plots/FDR_0.01_{antibody}consensus_{peak}-peaks"),
-            patterns=["{antibody}.{{group_1_vs_group_2}}.volcano-plot_FDR_0.01.pdf"],
+            patterns=["{antibody}.{group_1}_{antibody_1}_{control_1}vs{group_2}_{antibody_2}_{control_2}.volcano_FDR_0.01.pdf"],
             caption = "../report/plot_deseq2_FDR_1_perc_volcano.rst",
             category = "DESeq2"),
         plot_FDR_5_perc_volcano=report(
             directory("results/deseq2/comparison_plots/volcano_plots/FDR_0.05_{antibody}consensus_{peak}-peaks"),
-            patterns=["{antibody}.{{group_1_vs_group_2}}.volcano-plot_FDR_0.05.pdf"],
+            patterns=["{antibody}.{group_1}_{antibody_1}_{control_1}vs{group_2}_{antibody_2}_{control_2}.volcano_FDR_0.05.pdf"],
             caption = "../report/plot_deseq2_FDR_5_perc_volcano.rst",
             category = "DESeq2"),
         plot_sample_corr_heatmap=report(
             directory("results/deseq2/comparison_plots/correlation_heatmaps_{antibody}consensus_{peak}-peaks"),
-            patterns=["{antibody}.{{group_1_vs_group_2}}.correlation_heatmap.pdf"],
+            patterns=["{antibody}.{group_1}_{antibody_1}_{control_1}vs{group_2}_{antibody_2}_{control_2}.correlation_heatmap.pdf"],
             caption = "../report/plot_deseq2_sample_corr_heatmap.rst",
             category = "DESeq2"),
         plot_scatter=report(
             directory("results/deseq2/comparison_plots/scatter_plots_{antibody}consensus_{peak}-peaks"),
-            patterns=["{antibody}.{{group_1_vs_group_2}}.scatter_plots.pdf"],
+            patterns=["{antibody}.{group_1}_{antibody_1}_{control_1}vs{group_2}_{antibody_2}_{control_2}.scatter_plots.pdf"],
             caption = "../report/plot_deseq2_scatter.rst",
             category = "DESeq2")
     threads:
         2
     params:
-        vst = config["params"]["deseq2"]["vst"],
-        antibody = lambda w: w.antibody
+        vst = config["params"]["deseq2"]["vst"]
     log:
         "logs/deseq2/{antibody}.consensus_{peak}-peaks.featureCounts.log"
     conda:

workflow/rules/peak_analysis.smk

@@ -11,7 +11,7 @@ rule plot_fingerprint:
         fingerprint=report(
             "results/deeptools/{sample}-{control}.plot_fingerprint.pdf",
             caption="../report/plot_fingerprint_deeptools.rst",
-            category="QC"),
+            category="other QC"),
         counts="results/deeptools/{sample}-{control}.fingerprint_counts.txt",
         qc_metrics="results/deeptools/{sample}-{control}.fingerprint_qcmetrics.txt"
     log:

workflow/rules/qc.smk

@@ -16,7 +16,7 @@ rule multiqc:
     input:
         get_multiqc_input
     output:
-        report("results/qc/multiqc/multiqc.html", caption="../report/multiqc_report.rst", category="QC")
+        report("results/qc/multiqc/multiqc.html", caption="../report/multiqc_report.rst", category="MultiQC")
     log:
         "logs/multiqc.log"
     wrapper:

workflow/scripts/featurecounts_deseq2.R

@@ -285,7 +285,7 @@ if (file.exists(ResultsFile) == FALSE) {
 
                 ## WRITE RESULTS FILE
                 if (MIN_FDR == 0.01) {
-                    # AVI: dynamically file name extensions added
+                    # AVI: dynamically generated file name extensions added
                     dirs <- c(snakemake@output[["FDR_1_perc_res"]],snakemake@output[["FDR_1_perc_bed"]],snakemake@output[["plot_FDR_1_perc_MA"]],
                               snakemake@output[["plot_FDR_1_perc_volcano"]],snakemake@output[["FDR_5_perc_res"]],snakemake@output[["FDR_5_perc_bed"]],
                               snakemake@output[["plot_FDR_5_perc_MA"]],snakemake@output[["plot_FDR_5_perc_volcano"]],snakemake@output[["plot_sample_corr_heatmap"]],
@@ -296,19 +296,19 @@ if (file.exists(ResultsFile) == FALSE) {
                         }
                     }
 
-                    CompResultsFile <- paste(snakemake@output[["FDR_1_perc_res"]], "/", snakemake@params[["antibody"]], ".", CompPrefix, ".FDR_0.01_results.txt", sep="")
-                    CompBEDFile <- paste(snakemake@output[["FDR_1_perc_bed"]], "/", snakemake@params[["antibody"]], ".", CompPrefix, ".FDR_0.01_results.bed", sep="")
-                    MAplotFile <- paste(snakemake@output[["plot_FDR_1_perc_MA"]], "/", snakemake@params[["antibody"]], ".", CompPrefix, ".MA-plot_FDR_0.01.pdf", sep="")  # AVI: added to create separate pdf files
-                    VolcanoPlotFile <- paste(snakemake@output[["plot_FDR_1_perc_volcano"]], "/", snakemake@params[["antibody"]], ".", CompPrefix, ".volcano_FDR_0.01.pdf", sep="") # AVI: added to create separate pdf files
+                    CompResultsFile <- file.path(snakemake@output[["FDR_1_perc_res"]], paste(snakemake@params[["antibody"]], ".", CompPrefix, ".FDR_0.01_results.txt", sep=""))
+                    CompBEDFile <- file.path(snakemake@output[["FDR_1_perc_bed"]], paste(snakemake@wildcards[["antibody"]], ".", CompPrefix, ".FDR_0.01_results.bed", sep=""))
+                    MAplotFile <- file.path(snakemake@output[["plot_FDR_1_perc_MA"]], paste(snakemake@wildcards[["antibody"]], ".", CompPrefix, ".MA-plot_FDR_0.01.pdf", sep=""))  # AVI: added to create separate pdf files
+                    VolcanoPlotFile <- file.path(snakemake@output[["plot_FDR_1_perc_volcano"]], paste(snakemake@wildcards[["antibody"]], ".", CompPrefix, ".volcano_FDR_0.01.pdf", sep="")) # AVI: added to create separate pdf files
                 }
                 if (MIN_FDR == 0.05) {
                     # AVI: dynamically file name extensions added
-                    CompResultsFile <- paste(snakemake@output[["FDR_5_perc_res"]], "/", snakemake@params[["antibody"]], ".", CompPrefix, ".FDR_0.05_results.txt", sep="")
-                    CompBEDFile <- paste(snakemake@output[["FDR_5_perc_bed"]], "/", snakemake@params[["antibody"]], ".", CompPrefix, ".FDR_0.05_results.bed", sep="")
+                    CompResultsFile <- file.path(snakemake@output[["FDR_5_perc_res"]], paste(snakemake@wildcards[["antibody"]], ".", CompPrefix, ".FDR_0.05_results.txt", sep=""))
+                    CompBEDFile <- file.path(snakemake@output[["FDR_5_perc_bed"]], paste(snakemake@wildcards[["antibody"]], ".", CompPrefix, ".FDR_0.05_results.bed", sep=""))
                     # AVI: write paths of FDR 0.05 bed files to igv file
                     cat(paste0(CompBEDFile, "\t255,0,0\n"),file=snakemake@output[["igv_FDR_5_bed"]],append=TRUE)
-                    MAplotFile <- paste(snakemake@output[["plot_FDR_5_perc_MA"]], "/", snakemake@params[["antibody"]], ".", CompPrefix, ".MA-plot_FDR_0.05.pdf", sep="")   # AVI: added to create separate pdf files
-                    VolcanoPlotFile <- paste(snakemake@output[["plot_FDR_5_perc_volcano"]], "/", snakemake@params[["antibody"]], ".", CompPrefix, ".volcano_FDR_0.05.pdf", sep="")  # AVI: added to create separate pdf files
+                    MAplotFile <- file.path(snakemake@output[["plot_FDR_5_perc_MA"]], paste(snakemake@wildcards[["antibody"]], ".", CompPrefix, ".MA-plot_FDR_0.05.pdf", sep=""))   # AVI: added to create separate pdf files
+                    VolcanoPlotFile <- file.path(snakemake@output[["plot_FDR_5_perc_volcano"]], paste(snakemake@wildcards[["antibody"]], ".", CompPrefix, ".volcano_FDR_0.05.pdf", sep=""))  # AVI: added to create separate pdf files
                 }
 
                 write.table(pass.fdr.table, file=CompResultsFile, col.names=TRUE, row.names=FALSE, sep='\t', quote=FALSE)
@@ -335,7 +335,7 @@ if (file.exists(ResultsFile) == FALSE) {
         }
 
         ## SAMPLE CORRELATION HEATMAP
-        CorrHeatmapFile <- paste(snakemake@output[["plot_sample_corr_heatmap"]], "/", snakemake@params[["antibody"]], ".", CompPrefix, ".correlation_heatmap.pdf", sep="")  # AVI: dynamically file name extensions added
+        CorrHeatmapFile <- file.path(snakemake@output[["plot_sample_corr_heatmap"]], paste(snakemake@wildcards[["antibody"]], ".", CompPrefix, ".correlation_heatmap.pdf", sep=""))  # AVI: dynamically file name extensions added
         pdf(file=CorrHeatmapFile,width=10,height=8)  # AVI: added to create separate pdf files
         rld.subset <- assay(rld)[,comp.samples]
         sampleDists <- dist(t(rld.subset))
@@ -345,7 +345,7 @@ if (file.exists(ResultsFile) == FALSE) {
         dev.off()  # AVI: added to create separate pdf files
 
         ## SCATTER PLOT FOR RLOG COUNTS
-        ScatterPlotFile <- paste(snakemake@output[["plot_scatter"]], "/", snakemake@params[["antibody"]], ".", CompPrefix, ".scatter_plots.pdf", sep="")  # AVI: dynamically file name extensions added
+        ScatterPlotFile <- file.path(snakemake@output[["plot_scatter"]], paste(snakemake@wildcards[["antibody"]], ".", CompPrefix, ".scatter_plots.pdf", sep=""))  # AVI: dynamically file name extensions added
         pdf(file=ScatterPlotFile,width=10,height=8)  # AVI: added to create separate pdf files
         combs <- combn(comp.samples,2,simplify=FALSE)
         clabels <- sapply(combs,function(x){paste(x,collapse=' & ')})