Commit f653cb17 authored by Christian Arnold's avatar Christian Arnold

Version 1.1.1, see changelog for details

parent 03a4b949
......@@ -747,12 +747,13 @@ Stores various log and error files.
- ``*.log`` files from R scripts: Each log file is produced by the corresponding R script and contains debugging information as well as warnings and errors:
- ``1.produceConsensusPeaks.R.log``
- ``2.DiffPeaks.R.log``
- ``3.analyzeTF.{TF}.R.log`` for each TF ``{TF}``
- ``4.summary1.R.log``
- ``5.binningTF.{TF}.log`` for each TF ``{TF}``
- ``6.summaryFinal.R.log``
- ``checkParameterValidity.R.log``
- ``produceConsensusPeaks.R.log``
- ``diffPeaks.R.log``
- ``analyzeTF.{TF}.R.log`` for each TF ``{TF}``
- ``summary1.R.log``
- ``binningTF.{TF}.log`` for each TF ``{TF}``
- ``summaryFinal.R.log``
- ``*.log`` summary files: Summary logs for user convenience, produced at very end of the pipeline only. They should contain all errors and warnings from the pipeline run.
......@@ -972,9 +973,9 @@ If an R script fails with a technical error such as ``caught segfault`` (a segme
.. code-block:: R
snakemake = readRDS("{outputFolder}/LOGS_AND_BENCHMARKS/0.checkParameters.R.rds")
snakemake = readRDS("{outputFolder}/LOGS_AND_BENCHMARKS/checkParameters.R.rds")
Replace ``{outputFolder}`` by the folder you used for the analysis, and adjust the ``0.checkParameters`` part also accordingly. Essentially, you just have to provide the path to the corresponding file that is located in the ``LOGS_AND_BENCHMARKS`` subdirectly within the specified output directory.
Replace ``{outputFolder}`` by the folder you used for the analysis, and adjust the ``checkParameters`` part also accordingly. Essentially, you just have to provide the path to the corresponding file that is located in the ``LOGS_AND_BENCHMARKS`` subdirectly within the specified output directory.
Rerunning *Snakemake*
----------------------
......
......@@ -31,20 +31,22 @@ We also put the paper on *bioRxiv*, please read all methodological details here:
Change log
============================
Version 1.1.1 (2018-08-01, coming soon)
Version 1.1.1 (2018-08-01)
- Documentation updates (referenced the bioRxiv paper, extended the section about errors)
- updated the information on how to load the snakemake object into the R workspace in the corresponding R scripts
- fixed a small bug that made the Volcano plot and the circular one appear to have switched sides.
- fixed a bug that made the labels in the Volcano plot switch sides (thanks to Jonas Ungerbeck)
- merged some diagnostic plots for the AR classification in the last step
- renamed R scripts and R log files to make them consistent with the cluster output and error files
Version 1.1 (2018-07-27)
- added a new parameter *dir_TFBS_sorted* in the config file to specify that the TFBS input files are already sorted, which saves some computation time by not resorting them
- added a new parameter ``dir_TFBS_sorted`` in the config file to specify that the TFBS input files are already sorted, which saves some computation time by not resorting them
- updated the TFBS files that are available via download (some files were not presorted correctly)
- added support for single-end BAM files. There is a new parameter *pairedEnd* in the config file that specifies whether reads are paired-end or not.
- restructured some of the permutation-related output files to save space and computation time. The rule *concatenateMotifsPerm* should now be much faster, and the TF-specific *...outputPerm.tsv.gz* files are now much smaller due to an improved column structure
- added support for single-end BAM files. There is a new parameter ``pairedEnd`` in the config file that specifies whether reads are paired-end or not.
- restructured some of the permutation-related output files to save space and computation time. The rule ``concatenateMotifsPerm`` should now be much faster, and the TF-specific ``...outputPerm.tsv.gz`` files are now much smaller due to an improved column structure
Version 1.0.1 (2018-07-25)
- fixed a bug in *2.DiffPeaks.R* that sometimes caused the step to fail, thanks to Jonas Ungerbeck for letting us know
- fixed a bug in *3.analyzeTF* for rare corner cases when *DESeq* fails
- fixed a bug in ``2.DiffPeaks.R`` that sometimes caused the step to fail, thanks to Jonas Ungerbeck for letting us know
- fixed a bug in ``3.analyzeTF`` for rare corner cases when *DESeq* fails
Version 1.0 (2018-07-01)
- released stable version
......
......@@ -284,13 +284,13 @@ if config["par_general"]["nPermutations"] == 0 and config["par_general"]["nBoots
# Not to be confused with the dir_scripts directory, which is only used to load the correct functions.R file in all R scripts
dir_scripts = "R/"
script_checkParValidity = "0.checkParameters.R"
script_createConsensusPeaks = "1.createConsensusPeaks.R"
script_DiffPeaks = "2.DiffPeaks.R"
script_analyzeTF = "3.analyzeTF.R"
script_summary1 = "4.summary1.R"
script_binningTF = "5.binningTF.R"
script_summaryFinal = "6.summaryFinal.R"
script_checkParValidity = "checkParameterValidity.R"
script_createConsensusPeaks = "createConsensusPeaks.R"
script_DiffPeaks = "diffPeaks.R"
script_analyzeTF = "analyzeTF.R"
script_summary1 = "summary1.R"
script_binningTF = "binningTF.R"
script_summaryFinal = "summaryFinal.R"
......@@ -314,7 +314,7 @@ rule checkParameterValidity:
output:
flag = touch(TEMP_DIR + "/" + compType + "checkParameterValidity.done"),
consPeaks = TEMP_DIR + "/" + compType + "consensusPeaks.clean.bed",
log: expand('{dir}/0.checkParameters.R.log', dir = LOG_BENCHMARK_DIR)
log: expand('{dir}/checkParameterValidity.R.log', dir = LOG_BENCHMARK_DIR)
message: "{ruleDisplayMessage}Check parameter validity {script_checkParValidity}..."
threads: 1
priority: 1
......@@ -329,7 +329,7 @@ rule produceConsensusPeaks:
output:
consensusPeaks_bed = TEMP_DIR + "/" + compType + "consensusPeaks.bed",
summaryPlot = TEMP_DIR + "/" + compType + "consensusPeaks_lengthDistribution.pdf"
log: expand('{dir}/1.produceConsensusPeaks.R.log', dir = LOG_BENCHMARK_DIR)
log: expand('{dir}/produceConsensusPeaks.R.log', dir = LOG_BENCHMARK_DIR)
message: "{ruleDisplayMessage}Calculate consensus peaks for all peak files with the script {script_createConsensusPeaks}..."
threads: 1
params:
......@@ -520,7 +520,7 @@ rule DiffPeaks:
normCounts = PEAKS_DIR + "/" + compType + "countsNormalized.tsv.gz",
plots = name_plots,
DESeqObj = PEAKS_DIR + "/" + compType + "DESeq.object.rds"
log: expand('{dir}/2.DiffPeaks.R.log', dir = LOG_BENCHMARK_DIR)
log: expand('{dir}/DiffPeaks.R.log', dir = LOG_BENCHMARK_DIR)
message: "{ruleDisplayMessage}Run R script {script_DiffPeaks}"
threads: 1
params:
......@@ -543,7 +543,7 @@ rule analyzeTF:
outputPermTSV = TF_DIR + "/{TF}/" + extDir + "/" + compType + "{TF}.outputPerm.tsv.gz",
outputRDS = TF_DIR + "/{TF}/" + extDir + "/" + compType + "{TF}.summary.rds",
plot_diagnostic = name_plotsDiag
log: expand('{dir}/3.analyzeTF.{{TF}}.R.log', dir = LOG_BENCHMARK_DIR)
log: expand('{dir}/analyzeTF.{{TF}}.R.log', dir = LOG_BENCHMARK_DIR)
message: "{ruleDisplayMessage}Run R script {script_analyzeTF} for TF {wildcards.TF}..."
threads: 1
params:
......@@ -558,7 +558,7 @@ rule summary1:
TF = expand('{dir}/{TF}/{ext}/{compType}{TF}.summary.rds', dir = TF_DIR, TF = allTF, ext = extDir, compType = compType)
output:
outputTable = FINAL_DIR + "/" + compType + "TF_vs_peak_distribution.tsv.gz"
log: expand('{dir}/4.summary1.R.log', dir = LOG_BENCHMARK_DIR)
log: expand('{dir}/summary1.R.log', dir = LOG_BENCHMARK_DIR)
message: "{ruleDisplayMessage}Run R script {script_summary1} ..."
threads: 1
script: dir_scripts + script_summary1
......@@ -615,7 +615,7 @@ rule binningTF:
output:
permResults = expand('{dir}/{{TF}}/{extension}/{compType}{{TF}}.permutationResults.rds', dir = TF_DIR, extension = extDir, compType = compType),
summary = expand('{dir}/{{TF}}/{extension}/{compType}{{TF}}.permutationSummary.tsv.gz', dir = TF_DIR, extension = extDir, compType = compType)
log: expand('{dir}/5.binningTF.{{TF}}.R.log', dir = LOG_BENCHMARK_DIR)
log: expand('{dir}/binningTF.{{TF}}.R.log', dir = LOG_BENCHMARK_DIR)
message: "{ruleDisplayMessage}Run R script {script_binningTF} for TF {wildcards.TF}..."
threads: 1
script: dir_scripts + script_binningTF
......@@ -624,7 +624,7 @@ rule binningTF:
allDiagnosticFiles = []
allDiagnosticFiles.append(FINAL_DIR + "/" + compType + "diagnosticPlots.pdf")
if config["par_general"]["RNASeqIntegration"]:
classificationFiles = expand("{dir}/{compType}diagnosticPlotsClassification{no}.pdf", dir = FINAL_DIR, compType = compType, no = [1,2,3,4])
classificationFiles = expand("{dir}/{compType}diagnosticPlotsClassification{no}.pdf", dir = FINAL_DIR, compType = compType, no = [1,2])
allDiagnosticFiles.append(classificationFiles)
......@@ -640,7 +640,7 @@ rule summaryFinal:
volcanoPlot = FINAL_DIR + "/" + compType + "summary.volcano.pdf",
diagnosticPlots = allDiagnosticFiles,
plotsRDS = FINAL_DIR + "/" + compType + "summary.circular.rds",
log: expand('{dir}/6.summaryFinal.R.log', dir = LOG_BENCHMARK_DIR)
log: expand('{dir}/summaryFinal.R.log', dir = LOG_BENCHMARK_DIR)
message: "{ruleDisplayMessage}Run R script {script_summaryFinal} ..."
threads: 1
params: TFs = ",".join(allTF)
......
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