nf-core/cutandrun: nf-core/cutandrun v3.1 Lead Rooster

[3.1] - 2023-03-10 Major Changes 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 Updated pipeline template to nf-core/tools 2.7.2. Updated pipeline syntax to conform to new Nextflow version standards. Some locally defined subworkflows/modules have now been added to nf-core and re-imported as official modules/subworkflows. 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 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. Pipeline will now fail gracefully when single-end reads are detected. Software dependencies Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Dependency Old version New version 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. NB: Dependency has been removed if version information isn't present