Merge pull request #1075 from nf-core/patch

Fix issue with MQC not displaying post-ar trimming FastQC results

Author: TCLamnidis

.github/workflows/ci.yml

@@ -37,13 +37,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:2.5.1
+        run: docker build --no-cache . -t nfcore/eager:2.5.2
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.5.1
+          docker tag nfcore/eager:dev nfcore/eager:2.5.2
 
       - name: Install Nextflow
         env:

CHANGELOG.md

@@ -3,6 +3,20 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [2.5.2] - 2024-06-28
+
+### `Added`
+
+- [#1079](https://github.com/nf-core/eager/issues/1079) - Added the `lanemerging` output directory in the output documentation (♥ to @TessaZei for reporting, fix by @TCLamnidis).
+
+### `Fixed`
+
+- [#1037](https://github.com/nf-core/eager/issues/1073) - Fixed post-adapterremoval trimmed FastQC results not being displayed in MultiQC (♥ to @kieren-j-mitchell for reporting, fix by @jfy133 and @TCLamnidis)
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## [2.5.1] - 2024-02-21
 
 ### `Added`

Dockerfile

@@ -7,7 +7,7 @@ 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-2.5.1/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.5.2/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.5.1 > nf-core-eager-2.5.1.yml
+RUN conda env export --name nf-core-eager-2.5.2 > nf-core-eager-2.5.2.yml

assets/multiqc_config.yaml

@@ -74,6 +74,7 @@ top_modules:
       path_filters:
         - "*.truncated_fastqc.zip"
         - "*.combined*_fastqc.zip"
+        - "*_postartrimmed_fastqc.zip"
   - "bowtie2":
       path_filters:
         - "*_bt2.log"

docs/output.md

@@ -680,6 +680,7 @@ Each module has it's own output directory which sit alongside the `MultiQC/` dir
   * When masking of the reference is requested prior to running pmdtools, an additional directory `reference_genome/masked_genome` will be found here, containing the masked reference.
 * `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.
+* `lanemerging/`: this contains adapter-trimmed and merged (i.e. collapsed) FASTQ files that were merged across lanes, where applicable. These files are the reads that go into mapping (when multiple lanes were specified for a library), and can be used 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 `.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.

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-2.5.1
+name: nf-core-eager-2.5.2
 channels:
   - conda-forge
   - bioconda

nextflow.config

@@ -289,7 +289,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/eager:2.5.1'
+process.container = 'nfcore/eager:2.5.2'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -419,7 +419,7 @@ manifest {
   description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.07.1'
-  version = '2.5.1'
+  version = '2.5.2'
 }
 
 // Function to ensure that resource requirements don't go beyond