Merge branch 'dev' into empty-tsv-column

Author: apeltzer

CHANGELOG.md

@@ -13,8 +13,11 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#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
-- [#673](https://github.com/nf-core/eager/pull/673) - Fix Kraken database loading when loading from directory instead of compressed file
 - [#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.
 
 ### `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

nextflow.config

@@ -234,7 +234,7 @@ params {
   help = false
   igenomes_base = 's3://ngi-igenomes/igenomes/'
   tracedir = "${params.outdir}/pipeline_info"
-  igenomes_ignore = false
+  igenomes_ignore = true
   custom_config_version = 'master'
   custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
   hostnames = false

nextflow_schema.json

@@ -95,9 +95,9 @@
                 },
                 "genome": {
                     "type": "string",
-                    "description": "Name of iGenomes reference (required if not FASTA reference).",
+                    "description": "Name of iGenomes reference (required if not FASTA reference). Requires argument `--igenomes_ignore false` as iGenomes ignored by default in nf-core/eager",
                     "fa_icon": "fas fa-book",
-                    "help_text": "Alternatively to `--fasta`, the pipeline config files come bundled with paths to the Illumina iGenomes reference index files. If running with docker or AWS, the configuration is set up to use the [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) resource.\n\nThere are 31 different species supported in the iGenomes references. To run the pipeline, you must specify which to use with the `--genome` flag.\n\nYou can find the keys to specify the genomes in the [iGenomes config file](../conf/igenomes.config). Common genomes that are supported are:\n\n- Human\n  - `--genome GRCh37`\n  - `--genome GRCh38`\n- Mouse *\n  - `--genome GRCm38`\n- _Drosophila_ *\n  - `--genome BDGP6`\n- _S. cerevisiae_ *\n  - `--genome 'R64-1-1'`\n\n> \\* Not bundled with nf-core eager by default.\n\nNote that you can use the same configuration setup to save sets of reference files for your own use, even if they are not part of the iGenomes resource. See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for instructions on where to save such a file.\n\nThe syntax for this reference configuration is as follows:\n\n```nextflow\nparams {\n  genomes {\n    'GRCh37' {\n      fasta   = '<path to the iGenomes genome fasta file>'\n    }\n    // Any number of additional genomes, key is used with --genome\n  }\n}\n```"
+                    "help_text": "Alternatively to `--fasta`, the pipeline config files come bundled with paths to the Illumina iGenomes reference index files. If running with docker or AWS, the configuration is set up to use the [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) resource.\n\nThere are 31 different species supported in the iGenomes references. To run the pipeline, you must specify which to use with the `--genome` flag.\n\nYou can find the keys to specify the genomes in the [iGenomes config file](../conf/igenomes.config). Common genomes that are supported are:\n\n- Human\n  - `--genome GRCh37`\n  - `--genome GRCh38`\n- Mouse *\n  - `--genome GRCm38`\n- _Drosophila_ *\n  - `--genome BDGP6`\n- _S. cerevisiae_ *\n  - `--genome 'R64-1-1'`\n\n> \\* Not bundled with nf-core eager by default.\n\nNote that you can use the same configuration setup to save sets of reference files for your own use, even if they are not part of the iGenomes resource. See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for instructions on where to save such a file.\n\nThe syntax for this reference configuration is as follows:\n\n```nextflow\nparams {\n  genomes {\n    'GRCh37' {\n      fasta   = '<path to the iGenomes genome fasta file>'\n    }\n    // Any number of additional genomes, key is used with --genome\n  }\n}\n**NB** Requires argument `--igenomes_ignore false` as iGenomes ignored by default in nf-core/eager\n\n```"
                 },
                 "igenomes_base": {
                     "type": "string",