Merge branch 'dev' into master

Author: alexandregilardet

.github/workflows/ci.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['20.04.0', '']
+        nxf_ver: ['20.07.1', '']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -34,13 +34,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:2.3.1
+        run: docker build --no-cache . -t nfcore/eager:dev
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.3.1
+          docker tag nfcore/eager:dev nfcore/eager:dev
 
       - name: Install Nextflow
         env:

CHANGELOG.md

@@ -10,18 +10,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Fixed`
 
 - [#690](https://github.com/nf-core/eager/pull/690) - Fixed ANGSD output mode for beagle by setting `-doMajorMinor 1` as default in that case
-- [#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
-- [#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.
-- [#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.
-- 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
 
 ### `Dependencies`
 

Dockerfile

@@ -7,10 +7,10 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-eager-2.3.1/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.3.2dev/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.3.1 > nf-core-eager-2.3.1.yml
+RUN conda env export --name nf-core-eager-2.3.2dev > nf-core-eager-2.3.2dev.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

README.md

@@ -1,10 +1,10 @@
-# ![nf-core/eager](docs/images/nf-core-eager_logo.png)
+# ![nf-core/eager](docs/images/nf-core_eager_logo.png)
 
 **A fully reproducible and state-of-the-art ancient DNA analysis pipeline**.
 
 [![GitHub Actions CI Status](https://github.com/nf-core/eager/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/eager/actions)
 [![GitHub Actions Linting Status](https://github.com/nf-core/eager/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/eager/actions)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.04.0-brightgreen.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.07.1-brightgreen.svg)](https://www.nextflow.io/)
 [![nf-core](https://img.shields.io/badge/nf--core-pipeline-brightgreen.svg)](https://nf-co.re/)
 [![DOI](https://zenodo.org/badge/135918251.svg)](https://zenodo.org/badge/latestdoi/135918251)
 
@@ -159,6 +159,8 @@ of this pipeline:
 Those who have provided conceptual guidance, suggestions, bug reports etc.
 
 * Arielle Munters
+* [Charles Plessy](https://github.com/charles-plessy)
+* [Åshild Vågene](https://github.com/ashildv)
 * [Hester van Schalkwyk](https://github.com/hesterjvs)
 * [Ido Bar](https://github.com/IdoBar)
 * [Irina Velsko](https://github.com/ivelsko)

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'
 
@@ -74,38 +74,34 @@ 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, 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' }
-  }
-
-  withName: multiqc {
-    errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
+    errorStrategy = { task.exitStatus in [143,137,104,134,139, 140] ? 'ignore' : 'retry' }
   }
 
 }

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

environment.yml

@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-eager-2.3.1
+name: nf-core-eager-2.3.2dev
 channels:
   - conda-forge
   - bioconda