Merge branch 'dev' of github.com:nf-core/eager into dev

Author: maxibor

CHANGELOG.md

@@ -8,21 +8,32 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Added`
 
 - [#687](https://github.com/nf-core/eager/pull/687) - Adds Kraken2 unique kmer counting report
+- [#676](https://github.com/nf-core/eager/issues/676) - Refactor help message / summary message formatting to automatic versions using nf-core library
+- [#682](https://github.com/nf-core/eager/issues/682) - Add AdapterRemoval `--qualitymax` flag to allow FASTQ Phred score range max more than 41
 
 ### `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
 - Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv
-- [#652](https://github.com/nf-core/eager/issues/652) Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data
+- [#652](https://github.com/nf-core/eager/issues/652) - Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data
 - [#626](https://github.com/nf-core/eager/issues/626) - Add additional checks to ensure pipeline will give useful error if cells of a TSV column are empty
-- 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.
+- 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
 - [#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.
+- [#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
+- Added exit code `140` to re-tryable exit code list to account for certain scheduler wall-time limit fails
+- [672](https://github.com/nf-core/eager/issues/672) - Removed java parameter from picard tools which could cause memory issues
+- [679](https://github.com/nf-core/eager/issues/679) - Refactor within-process bash conditions to groovy/nextflow, due to incompatibility with some servers environments
+- [#690](https://github.com/nf-core/eager/pull/690) - Fixed ANGSD output mode for beagle by setting `-doMajorMinor 1` as default in that case
+- [#693](https://github.com/nf-core/eager/issues/693) - Fixed broken TSV input validation for the Colour Chemistry column
+- [#695](https://github.com/nf-core/eager/issues/695) - Fixed incorrect `-profile` order in tutorials (originally written reversed due to [nextflow bug](https://github.com/nextflow-io/nextflow/issues/1792))
 
 ### `Dependencies`
 
+- Bumped MultiQC to 1.10 for improved functionality
+- Bumped HOPS to 0.35 for MultiQC 1.10 compatibility
+
 ### `Deprecated`
 
 ## [2.3.1] - 2021-01-14

README.md

@@ -158,6 +158,7 @@ of this pipeline:
 
 Those who have provided conceptual guidance, suggestions, bug reports etc.
 
+* [Alexandre Gilardet](https://github.com/alexandregilardet)
 * Arielle Munters
 * [Charles Plessy](https://github.com/charles-plessy)
 * [Åshild Vågene](https://github.com/ashildv)

conf/base.config

@@ -14,7 +14,7 @@ process {
   memory = { check_max( 7.GB * task.attempt, 'memory' ) }
   time = { check_max( 24.h * task.attempt, 'time' ) }
 
-  errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+  errorStrategy = { task.exitStatus in [143,137,104,134,139, 140] ? 'retry' : 'finish' }
   maxRetries = 3
   maxErrors = '-1'
 
@@ -74,34 +74,34 @@ process {
   }
 
   withName:qualimap{
-    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139, 140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
   }
 
   withName:preseq {
     errorStrategy = 'ignore'
   }
 
   withName:damageprofiler {
-    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139, 140] ? 'retry' : 'finish' }
   }
 
   // Add 1 retry for certain java tools as not enough heap space java errors gives exit code 1
   withName: dedup {
-    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' } 
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139, 140] ? 'retry' : 'finish' } 
   }
 
   withName: markduplicates {
-    errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'finish' } 
+    errorStrategy = { task.exitStatus in [143,137, 140] ? 'retry' : 'finish' } 
   }
 
   // Add 1 retry as not enough heapspace java error gives exit code 1
   withName: malt {
-    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' } 
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139, 140] ? 'retry' : 'finish' } 
   }
 
   // other process specific exit statuses
   withName: nuclear_contamination {
-    errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'ignore' : 'retry' }
+    errorStrategy = { task.exitStatus in [143,137,104,134,139, 140] ? 'ignore' : 'retry' }
   }
 
 }