From af3bf3c41dccdb194aa0c370e2f5e6871b379587 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 9 Mar 2023 15:35:35 +0000 Subject: [PATCH 1/5] Update schema --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 7bd56d57..0dac5f4b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -346,7 +346,7 @@ "type": "number", "default": 0.05, "fa_icon": "fas fa-align-justify", - "description": "SEACR specifies a numeric threshold of n between 0 and 1 returns the top n fraction of peaks based on total signal within peaks. This is only used if there are no controls included with the samples and if `--use_control` is `false`" + "description": "SEACR specifies returns the top n fraction (between 0 and 1) of peaks based on total signal within peaks. This is only used if there are no controls included with the samples and if `--use_control` is `false`" }, "seacr_norm": { "type": "string", From 1845f778b8aac8d087824c77def8bfbf53cbf050 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 9 Mar 2023 15:36:17 +0000 Subject: [PATCH 2/5] Update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6c42ee0d..cc3b5035 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,7 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixes - Fixed confusing config warnings that were being displayed on legitmate parameter configurations. -- Fixed deeptools correlation plots that were showing low levels of correlation even in test data by changing the plot to use the pearson test. +- Fixed deeptools correlation plots that were showing low levels of correlation even in test data by changing the plot to use Pearson correlation. - Corrected the SEACR p-value parameter description. - Fixed output of picard mark/remove duplicate files so that the sorted, indexed bams for all files always output to the results folder. - Spikein genome processes and checks no longer run when the normalisation mode is set to something other than `SpikeIn`. From 7e77fd865fde0d85d9d5ab1743b161c9eeba1be6 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 9 Mar 2023 15:36:49 +0000 Subject: [PATCH 3/5] Update chanelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cc3b5035..be42481a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,7 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed confusing config warnings that were being displayed on legitmate parameter configurations. - Fixed deeptools correlation plots that were showing low levels of correlation even in test data by changing the plot to use Pearson correlation. - Corrected the SEACR p-value parameter description. -- Fixed output of picard mark/remove duplicate files so that the sorted, indexed bams for all files always output to the results folder. +- Fixed output of Picard mark/remove duplicate files so that the sorted, indexed bams for all files always output to the results folder. - Spikein genome processes and checks no longer run when the normalisation mode is set to something other than `SpikeIn`. - Pipeline will now fail gracefully when single-end reads are detected. From 7e5607eef5e4b9226d7d481b88b3d90df84c6464 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 9 Mar 2023 15:38:38 +0000 Subject: [PATCH 4/5] Update changelog --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index be42481a..a353ccc9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,8 +32,8 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi | Dependency | Old version | New version | | ---------- | ----------- | ----------- | -| `multiqc` | 1.14 | 1.16.1 | -| `samtools` | 2.27.2 | 2.27.4 | +| `multiqc` | 1.13 | 1.14 | +| `samtools` | 1.15.1 | 1.16.1 | > **NB:** Dependency has been **updated** if both old and new version information is present. > **NB:** Dependency has been **added** if just the new version information is present. From f5db8302a7fa4206e3bfb8547d0e4b642530d089 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 9 Mar 2023 21:02:19 +0000 Subject: [PATCH 5/5] Update default bowtie2 parameters --- CHANGELOG.md | 1 + conf/modules.config | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a353ccc9..7eb54419 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - IgG controls will now be analysed by the deeptools QC subworkflow giving greater visibility on the quality of control samples. - Updated the MACS2 default parameters to better process PA-Tn5/PA-Mnase based experiments. The new defaults use the q-value of `0.01` as the default cutoff in place of the p-value. The defaults have also been updated to keep duplicate reads int he peak finding process and also to shift the model to better account for nucleosome positioning `--nomodel --shift -75 --extsize 150 --keep-dup all` - Deeptools plotHeatmap will now run for all samples as well as for singles. This can be disabled using the parameter `--dt_calc_all_matrix false` +- Bowtie2 default parameters have been updated to use the `--dovetail` option. After careful consideration and literature review, we have decided that overlapping mates can occur in CUT&RUN data and are still valid reads. This is also the agreed parameterisation in similar pipelines and also on the 4D nucleome portal. ### Enhancements diff --git a/conf/modules.config b/conf/modules.config index fd93d1c0..f4ea027a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -240,7 +240,7 @@ if(params.run_trim_galore_fastqc && !params.skip_trimming) { if(params.run_alignment) { process { withName: '.*:ALIGN_BOWTIE2:BOWTIE2_TARGET_ALIGN' { - ext.args = { params.skip_trimming ? '--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 --minins 10 --maxins 700' : '--local --very-sensitive --no-mixed --no-discordant --phred33 --minins 10 --maxins 700' } + ext.args = { params.skip_trimming ? '--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 --minins 10 --maxins 700 --dovetail' : '--local --very-sensitive --no-mixed --no-discordant --phred33 --minins 10 --maxins 700 --dovetail' } publishDir = [ [ path: { "${params.outdir}/02_alignment/${params.aligner}/target/log" },