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TASK-6324 - Simplify QC analysis by launching a single job #2469

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833d0f3
analysis: update alignment QC analysis in order to launch a single jo…
jtarraga May 31, 2024
483c1be
Merge branch 'develop' into TASK-6324
jtarraga Jun 13, 2024
b0aea7b
app: fix circos.R and move to app/analysis/genome-plot, #TASK-6326, #…
jtarraga Jun 14, 2024
333e6dc
analysis: add FastQC docker cli in the result.json file, and remove u…
jtarraga Jun 18, 2024
177f1a2
analysis: add Samtools docker CLI in the result.json file, and remove…
jtarraga Jun 18, 2024
512c17d
analysis: use ToolRunner to execute each alignment QC step (i.e.: sam…
jtarraga Jun 18, 2024
65a1bdd
analysis: support the flag overwrite, and forward excetions, and mino…
jtarraga Jun 18, 2024
55c81ff
test: add JUnit tests for alignment QC, #TASK-6325, #TASK-6324
jtarraga Jun 18, 2024
0d78abd
analysis: add docker CLI and parameters in the tool step, fix some ty…
jtarraga Jun 19, 2024
af024c6
analysis: add parameters in the tool step, #TASK-6326, #TASK-6324
jtarraga Jun 19, 2024
edb882b
analysis: add docker CLI and parameters in the tool step (in genome p…
jtarraga Jun 19, 2024
39c2f6a
analysis: add the method addStepAttributes, #TASK-6326, #TASK-6324
jtarraga Jun 19, 2024
7e3ca47
analysis: use the ToolRunner instead of launching jobs for each sampl…
jtarraga Jun 19, 2024
f88c703
analysis: remove unused get/set methods and R scripts, #TASK-6325, #T…
jtarraga Jun 19, 2024
aed7911
analysis: update circos/genome plot to take the R script from the ana…
jtarraga Jun 19, 2024
592c793
tests: add and update JUnit tests for sample QC, #TASK-6326, #TASK-6324
jtarraga Jun 19, 2024
11a8653
Merge branch 'develop' into TASK-6324
jtarraga Jun 19, 2024
9f6913b
analysis: add a new tool step to update the alignment QC, #TASK-6325,…
jtarraga Jun 19, 2024
4518a72
analysis: minor improvements in sample QC analysis, #TASK-6326, #TASK…
jtarraga Jun 19, 2024
06d46a7
analysis: read the stderr file to get error messages when something w…
jtarraga Jun 20, 2024
37faea0
analysis: add the result of the "nested" analysis to the current step…
jtarraga Jun 21, 2024
0531c48
analysis: use a simpler ToolRunner constructor, #TASK-6325, #TASK-6324
jtarraga Jun 21, 2024
a53bd04
analysis: use a simpler ToolRunner constructor, #TASK-6326, #TASK-6324
jtarraga Jun 21, 2024
f77ca2e
Merge branch 'release-3.2.x' into TASK-6324
jtarraga Jul 22, 2024
8666ba9
Merge branch 'release-3.2.x' into TASK-6324
jtarraga Aug 14, 2024
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Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,7 @@ protected void run() throws ToolException {
});
}

public static FastQcMetrics parseResults(Path outDir) throws ToolException {
public static FastQcMetrics parseResults(Path outDir, String confJobDir) throws ToolException {
Path fastQcPath = null;
Path imgPath = null;
for (java.io.File file : outDir.toFile().listFiles()) {
Expand All @@ -116,8 +116,11 @@ public static FastQcMetrics parseResults(Path outDir) throws ToolException {
// Replace absolute paths to relative paths
List<String> relativePaths = new ArrayList<>();
for (String path : fastQcMetrics.getFiles()) {
int index = path.indexOf("JOBS/");
relativePaths.add(index == -1 ? new java.io.File(path).getName() : path.substring(index));
// Sanity check
if (!path.startsWith(confJobDir)) {
throw new ToolException("The FastQC file " + path + " is not in the configuration job folder "+ confJobDir);
}
relativePaths.add(path.substring(confJobDir.length() + 1));
}
fastQcMetrics.setFiles(relativePaths);
} else {
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