Merge pull request #896 from nf-core/output-docs-improvements

Output docs improvements

Author: jfy133

CHANGELOG.md

@@ -7,14 +7,15 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
+
 ### `Fixed`
 
 - [#882](https://github.com/nf-core/eager/pull/882) Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian)
 - [#879](https://github.com/nf-core/eager/issues/879) Add missing threads parameter for pre-clipping FastQC for single end data that caused insufficient memory in some cases (♥ to @marcel-keller for reporting)
 - [#885](https://github.com/nf-core/eager/issues/885) Specify task memory for all tools in get_software_versions to account for incompatibilty of java with some SGE clusters causing hanging of the process (♥ to @maxibor for reporting)
 - [#887](https://github.com/nf-core/eager/issues/887) Clarify what is considered 'ultra-short' reads in the help text of clip_readlength, for when you may wish to turn of length filtering during AdapterRemoval (♥ to @TCLamnidis for reporting)
 - [#889](https://github.com/nf-core/eager/issues/889) Remove/updated parameters from benchmarking test profiles (♥ to @TCLamnidis for reporting)
-
+- [#895](https://github.com/nf-core/eager/issues/895) Output documentation typo fix and added location of output docs in pipeline summary (♥ to @RodrigoBarquera for reporting)
 
 ### `Dependencies`
 

docs/output.md

@@ -679,7 +679,7 @@ Each module has it's own output directory which sit alongside the `MultiQC/` dir
 * `fastqc/`: this contains the original per-FASTQ FastQC reports that are summarised with MultiQC. These occur in both `html` (the report) and `.zip` format (raw data). The `after_clipping` folder contains the same but for after AdapterRemoval.
 * `adapterremoval/`: this contains the log files (ending with `.settings`) with raw trimming (and merging) statistics after AdapterRemoval. In the `output` sub-directory, are the output trimmed (and merged) `fastq` files. These you can use for downstream applications such as taxonomic binning for metagenomic studies.
 * `post_ar_fastq_trimmed`: this contains `fastq` files that have been additionally trimmed after AdapterRemoval (if turned on). These reads are usually that had internal barcodes, or damage that needed to be removed before mapping.
-* `mapping/`: this contains a sub-directory corresponding to the mapping tool you used, inside of which will be the initial BAM files containing the reads that mapped to your reference genome with no modification (see below). You will also find a corresponding BAM index file (ending in `.csi` or `.bam`), and if running the `bowtie2` mapper: a log ending in `_bt2.log`. You can use these for downstream applications e.g. if you wish to use a different de-duplication tool not included in nf-core/eager (although please feel free to add a new module request on the Github repository's [issue page](https://github.com/nf-core/eager/issues)!).
+* `mapping/`: this contains a sub-directory corresponding to the mapping tool you used, inside of which will be the initial BAM files containing the reads that mapped to your reference genome with no modification (see below). You will also find a corresponding BAM index file (ending in `.csi` or `.bai`), and if running the `bowtie2` mapper: a log ending in `_bt2.log`. You can use these for downstream applications e.g. if you wish to use a different de-duplication tool not included in nf-core/eager (although please feel free to add a new module request on the Github repository's [issue page](https://github.com/nf-core/eager/issues)!).
 * `samtools/`: this contains two sub-directories. `stats/` contain the raw mapping statistics files (ending in `.stats`) from directly after mapping. `filter/` contains BAM files that have had a mapping quality filter applied (set by the `--bam_mapping_quality_threshold` flag) and a corresponding index file. Furthermore, if you selected `--bam_discard_unmapped`, you will find your separate file with only unmapped reads in the format you selected. Note unmapped read BAM files will _not_ have an index file.
 * `deduplication/`: this contains a sub-directory called `dedup/`, inside here are sample specific directories. Each directory contains a BAM file containing mapped reads but with PCR duplicates removed, a corresponding index file and two stats file. `.hist.` contains raw data for a deduplication histogram used for tools like preseq (see below), and the `.log` contains overall summary deduplication statistics.
 * `endorSpy/`: this contains all JSON files exported from the endorSpy endogenous DNA calculation tool. The JSON files are generated specifically for display in the MultiQC general statistics table and is otherwise very likely not useful for you.

main.nf

@@ -3320,6 +3320,7 @@ workflow.onComplete {
     if (workflow.success) {
         log.info "-${c_purple}[nf-core/eager]${c_green} Pipeline completed successfully${c_reset}-"
         log.info "-${c_purple}[nf-core/eager]${c_green} MultiQC run report can be found in ${params.outdir}/multiqc ${c_reset}-"
+        log.info "-${c_purple}[nf-core/eager]${c_green} Further output documentation can be seen at https://nf-core/eager/output ${c_reset}-"
     } else {
         checkHostname()
         log.info "-${c_purple}[nf-core/eager]${c_red} Pipeline completed with errors${c_reset}-"