From 2597bcae78f1aba961a81b3b5c543849bf8b6f8a Mon Sep 17 00:00:00 2001 From: Lucas Czech Date: Tue, 10 Dec 2024 01:51:30 +0100 Subject: [PATCH] Refinements in trimmomatic config @meixilin --- config/config.yaml | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index be704e1..251967b 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -347,7 +347,7 @@ settings: # This also creates a file "mpileup/all-sample-names.txt", which lists the order of the # pileup columns in the file, which is the same order as the `data: samples-table` input table # (the order in which each sample name appears first in the table, forsamples with multiple units). - # - "all-sampless" + # - "all-samples" # # Make a pileup file with one column only, by merging all samples with all units into one pile. # - "all-merged-samples" @@ -473,11 +473,19 @@ params: # Used only if settings:trimming-tool == trimmomatic # See trimmomatic manual: http://www.usadellab.org/cms/?page=trimmomatic + # Download adapters here: https://github.com/usadellab/Trimmomatic/tree/main/adapters trimmomatic: threads: 6 se: extra: "" trimmer: + # We recommend playing with these settings, e.g., LEADING and TRAILING might be better at 5, + # and SLIDINGWINDOW might work better with, e.g., 4:20. + # Adapter sequences should be provided as in the ILLUMINACLIP examples; unfortunately, + # we cannot provide the standard adapter files within grenepipe due to copyrights. + # Change the `/path/to/...` to absolute paths as needed. + # - "ILLUMINACLIP:/path/to/adapters/TruSeq3-PE-2.fa:2:30:10:2:True" + # - "ILLUMINACLIP:/path/to/adapter-se.fa:2:30:10" - "LEADING:3" - "TRAILING:3" - "SLIDINGWINDOW:4:15" @@ -485,14 +493,12 @@ params: pe: extra: "" trimmer: - # We recommend playing with these settings, e.g., LEADING and TRAILING might be better at 5, - # and SLIDINGWINDOW might work better with, e.g., 4:20. - # Adapter sequences can also be provided as in the ILLUMINACLIP example below. + # Same as above for the single end trimming. See there for details. + # - "ILLUMINACLIP:/path/to/adapter-pe.fa:2:30:10:2:True" - "LEADING:3" - "TRAILING:3" - "SLIDINGWINDOW:4:15" - "MINLEN:36" - # - "ILLUMINACLIP:/path/to/adapters/TruSeq3-PE-2.fa:2:30:10:2:True" # ---------------------------------------------------------------------- # bowtie2