diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e30b7d700..45e4f2186 100644 --- a/.github/workflows/ci.yml +++ b/.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: ${{ !env.MATCHED_FILES }} run: | docker pull nfcore/eager:dev - docker tag nfcore/eager:dev nfcore/eager:2.5.1 + docker tag nfcore/eager:dev nfcore/eager:2.5.2 - name: Install Nextflow env: diff --git a/CHANGELOG.md b/CHANGELOG.md index 2da3a8c47..4ae9c442b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,20 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). +## [2.5.2] - 2024-06-28 + +### `Added` + +- [#1079](https://github.com/nf-core/eager/issues/1079) - Added the `lanemerging` output directory in the output documentation (♥ to @TessaZei for reporting, fix by @TCLamnidis). + +### `Fixed` + +- [#1037](https://github.com/nf-core/eager/issues/1073) - Fixed post-adapterremoval trimmed FastQC results not being displayed in MultiQC (♥ to @kieren-j-mitchell for reporting, fix by @jfy133 and @TCLamnidis) + +### `Dependencies` + +### `Deprecated` + ## [2.5.1] - 2024-02-21 ### `Added` diff --git a/Dockerfile b/Dockerfile index 01194d7b3..99b967439 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,7 +7,7 @@ COPY environment.yml / RUN conda env create --quiet -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-eager-2.5.1/bin:$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 \ No newline at end of file +RUN conda env export --name nf-core-eager-2.5.2 > nf-core-eager-2.5.2.yml \ No newline at end of file diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml index 8804ed9e1..f02837427 100644 --- a/assets/multiqc_config.yaml +++ b/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" diff --git a/docs/output.md b/docs/output.md index 9ad6cb9ba..b17aa8253 100644 --- a/docs/output.md +++ b/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. diff --git a/environment.yml b/environment.yml index f9eb8f0b9..3f777f1d9 100644 --- a/environment.yml +++ b/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 diff --git a/nextflow.config b/nextflow.config index 97308f807..2dddcaf30 100644 --- a/nextflow.config +++ b/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