Merge pull request #678 from nf-core/qualimap-empty-bam-fix

Qualimap empty bam fix

Author: apeltzer

CHANGELOG.md

@@ -10,10 +10,11 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Fixed`
 
 - [#666](https://github.com/nf-core/eager/issues/666) - Fixed input file staging for `print_nuclear_contamination`
-- [#631](https://github.com/nf-core/eager/issues/631): - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled
+- [#631](https://github.com/nf-core/eager/issues/631) - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled
 - Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv
 - Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data.  `
-- [#673](https://github.com/nf-core/eager/pull/673) - Fix Kraken database loading when loading from directory instead of compressed file.
+- [#673](https://github.com/nf-core/eager/pull/673) Fix Kraken database loading when loading from directory instead of compressed file.
+- [#688](https://github.com/nf-core/eager/issues/668) - Allow pipeline to complete, even if Qualimap crashes due to an empty or corrupt BAM file for one sample/library
 - [#683](https://github.com/nf-core/eager/pull/683) - Sets `--igenomes_ignore` to true by default, as rarely used by users currently and makes resolving configs less complex.
 
 ### `Dependencies`

conf/base.config

@@ -74,7 +74,7 @@ process {
   }
 
   withName:qualimap{
-    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
   }
 
   withName:preseq {

docs/output.md

@@ -551,6 +551,8 @@ Note that many of the statistics from this module are displayed in the General S
 
 You will receive output for each *sample*. This means you will statistics of deduplicated values of all types of libraries combined in a single value (i.e. non-UDG treated, full-UDG, paired-end, single-end all together).
 
+:warning: If your library has no reads mapping to the reference, this will result in an empty BAM file. Qualimap will therefore not produce any output even if a BAM exists!
+
 #### Coverage Histogram
 
 This plot shows on the Y axis the range of fold coverages that the bases of the reference genome are possibly covered by. The Y axis shows the number of bases that were covered at the given fold coverage depth as indicated on the Y axis.

docs/usage.md

@@ -413,6 +413,14 @@ they are unique (e.g. if one library was sequenced on Lane 8 of two HiSeq runs,
 specify lanes as 8 and 16 for each FASTQ file respectively). For library merging
 errors, you must modify your `Library_ID`s accordingly, to make them unique.
 
+### A library or sample is missing in my MultiQC report
+
+In some cases it maybe no output log is produced by a particular tool for MultiQC. Therefore this sample will not be displayed.
+
+Known cases include:
+
+- Qualimap: there will be no MultiQC output if the BAM file is empty. An empty BAM file causes Qualimap to crash - this is crash is ignored by nf-core/eager (to allow the rest of the pipeline to continue) and will therefore have no log file for that particular sample/library
+
 ## Tutorials
 
 ### Tutorial - How to investigate a failed run