From 8ce77e5d4fe003366c5d272c2c6b14abedcbcdb1 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 7 Jun 2024 14:53:21 +0200 Subject: [PATCH 1/3] Fix issue with MQC not displaying post-ar trimming FastQC results --- CHANGELOG.md | 14 +++++++++++++- assets/multiqc_config.yaml | 1 + 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2da3a8c47..92739eeaf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,18 @@ 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] - 2024-06-07 + +### `Added` + +### `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` @@ -11,7 +23,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` -- [#1048](https://github.com/nf-core/eager/issues/1048) `--vcf2genome_outfile` parameter now gets prefixed by the sample_name and suffixed with `.fasta` (i.e. `_.fasta`). This ensures we avoid overwriting the output fasta of one sample with that of another when the option is provided. (♥ Thanks to @MeriamOs for reporting.) +- [#1048](https://github.com/nf-core/eager/issues/1048) `--vcf2genome_outfile` parameter now gets prefixed by the sample*name and suffixed with `.fasta` (i.e. `*.fasta`). This ensures we avoid overwriting the output fasta of one sample with that of another when the option is provided. (♥ Thanks to @MeriamOs for reporting.) - [#1047](https://github.com/nf-core/eager/issues/1047) Changed the row some statistics were reported in the General Stats table. The File name collision fixed in 2.5.0 (see #1017) caused these statistics to be reported in the wrong row due to an added suffix. - [#1051](https://github.com/nf-core/eager/issues/1051) An error is now thrown if input BAM files end in `.unmapped.bam`, as this breaks the bam filtering process and empties the bam files in the process. (♥ Thanks to @PCQuilis for reporting.) 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" From bda3bda9bc0b0962aae62d55ea0a10606f97faeb Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 7 Jun 2024 14:54:58 +0200 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 92739eeaf..4266082fc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,7 +23,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` -- [#1048](https://github.com/nf-core/eager/issues/1048) `--vcf2genome_outfile` parameter now gets prefixed by the sample*name and suffixed with `.fasta` (i.e. `*.fasta`). This ensures we avoid overwriting the output fasta of one sample with that of another when the option is provided. (♥ Thanks to @MeriamOs for reporting.) +- [#1048](https://github.com/nf-core/eager/issues/1048) `--vcf2genome_outfile` parameter now gets prefixed by the sample\name and suffixed with `.fasta` (i.e. `_.fasta`). This ensures we avoid overwriting the output fasta of one sample with that of another when the option is provided. (♥ Thanks to @MeriamOs for reporting.) - [#1047](https://github.com/nf-core/eager/issues/1047) Changed the row some statistics were reported in the General Stats table. The File name collision fixed in 2.5.0 (see #1017) caused these statistics to be reported in the wrong row due to an added suffix. - [#1051](https://github.com/nf-core/eager/issues/1051) An error is now thrown if input BAM files end in `.unmapped.bam`, as this breaks the bam filtering process and empties the bam files in the process. (♥ Thanks to @PCQuilis for reporting.) From 9ba1f5bfc74265c9d48eb4a31672627f57bdb9f9 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 7 Jun 2024 15:38:19 +0200 Subject: [PATCH 3/3] Fix changelog autoformatting error --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4266082fc..2bac6b856 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,7 +23,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` -- [#1048](https://github.com/nf-core/eager/issues/1048) `--vcf2genome_outfile` parameter now gets prefixed by the sample\name and suffixed with `.fasta` (i.e. `_.fasta`). This ensures we avoid overwriting the output fasta of one sample with that of another when the option is provided. (♥ Thanks to @MeriamOs for reporting.) +- [#1048](https://github.com/nf-core/eager/issues/1048) `--vcf2genome_outfile` parameter now gets prefixed by the sample_name and suffixed with `.fasta` (i.e. `\_.fasta`). This ensures we avoid overwriting the output fasta of one sample with that of another when the option is provided. (♥ Thanks to @MeriamOs for reporting.) - [#1047](https://github.com/nf-core/eager/issues/1047) Changed the row some statistics were reported in the General Stats table. The File name collision fixed in 2.5.0 (see #1017) caused these statistics to be reported in the wrong row due to an added suffix. - [#1051](https://github.com/nf-core/eager/issues/1051) An error is now thrown if input BAM files end in `.unmapped.bam`, as this breaks the bam filtering process and empties the bam files in the process. (♥ Thanks to @PCQuilis for reporting.)