Merge pull request #665 from charles-plessy/patch-5

Document that `skip_collapse` turns on paired-end alignment.

Author: jfy133

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#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
+- Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data.  `
 
 ### `Dependencies`
 

README.md

@@ -159,6 +159,7 @@ 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)

nextflow_schema.json

@@ -472,9 +472,9 @@
                 },
                 "skip_collapse": {
                     "type": "boolean",
-                    "description": "Skip of merging forward and reverse reads together. Only applicable for paired-end libraries.",
+                    "description": "Skip of merging forward and reverse reads together and turns on paired-end alignment for downstream mapping. Only applicable for paired-end libraries.",
                     "fa_icon": "fas fa-fast-forward",
-                    "help_text": "Turns off the paired-end read merging.\n\nFor example\n\n```bash\n--skip_collapse  --input '*_{R1,R2}_*.fastq'\n```\n\nIt is important to use the paired-end wildcard globbing as `--skip_collapse` can only be used on paired-end data!\n\n:warning: If you run this and also with `--clip_readlength` set to something (as is by default), you may end up removing single reads from either the pair1 or pair2 file. These will be NOT be mapped when aligning with either `bwa` or `bowtie`, as both can only accept one (forward) or two (forward and reverse) FASTQs as input.\n\n> Modifies AdapterRemoval parameter: `--collapse`"
+                    "help_text": "Turns off the paired-end read merging.\n\nFor example\n\n```bash\n--skip_collapse  --input '*_{R1,R2}_*.fastq'\n```\n\nIt is important to use the paired-end wildcard globbing as `--skip_collapse` can only be used on paired-end data!\n\n:warning: If you run this and also with `--clip_readlength` set to something (as is by default), you may end up removing single reads from either the pair1 or pair2 file. These will be NOT be mapped when aligning with either `bwa` or `bowtie`, as both can only accept one (forward) or two (forward and reverse) FASTQs as input.\n\nAlso note that supplying this flag will also then cause downstream mapping steps to run in paired-end mode. This maybe more suitable for modern data, or when you want to utilise mate-pair spatial information.\n\n> Modifies AdapterRemoval parameter: `--collapse`"
                 },
                 "skip_trim": {
                     "type": "boolean",
@@ -1620,4 +1620,4 @@
             "$ref": "#/definitions/metagenomic_authentication"
         }
     ]
-}
+}