Simon Pearce
Simon Pearce
### Description of feature Samtools pileup has the config process label of `process_medium`, but is not parallelised at all. It requests 6 cores and 36GB of RAM by default, but...
The umi_tools dedup command is not currently deterministic, even if `--random-seed` is set, unless the `PYTHONHASHSEED` environment variable is also set. Detailed in [https://github.com/CGATOxford/UMI-tools/issues/440](url) and [https://github.com/CGATOxford/UMI-tools/pull/470](url). Not fixed in the...
--- name: Cancer Research UK Manchester Institute Config about: A new cluster config --- Please follow these steps before submitting your PR: - [ ] If your PR is a...
I propose that we rename the `bam_dedup_stats_samtools_umitools` subworkflow to be just `bam_dedup_umitools`. [Various](https://github.com/nf-core/modules/blob/a52cd7df53f3e88895362f2c8fd43cfe00fbf1a3/subworkflows/nf-core/fastq_align_bowtie2/main.nf#L6) [other](https://github.com/nf-core/modules/blob/master/subworkflows/nf-core/bam_markduplicates_picard/main.nf) [subworkflows](https://github.com/nf-core/modules/blob/master/subworkflows/nf-core/fastq_align_hisat2/main.nf) generate stats using `samtools`, without mentioning it in the name of the subworkflow. I think...
The new process tag `process_single` is not present in the tools options. There is a [part of a PR here](https://github.com/nf-core/tools/pull/1823), but not finished.
Swap the containers for GET_META and GET_PATH to use the base ubuntu image already pulled for CAT_FASTQ, as they are already pulled by the pipeline. Helps those who struggle to...
Hi ichorCNA team, I've been using the most recent version, v0.3.2, for a while with good results. I'm now trying to put ichorCNA into a nextflow module within the [nf-core](https://nf-co.re/)...
Firstly, I've found this tool is excellent at determining which samples are which, to verify that matched pairs are indeed matched. For the bam method, you currently have the location...
### Description of the bug ngscheckmate_bed is set incorrectly for GATK.GRCh37 - this genome has no "chr". ### Command used and terminal output _No response_ ### Relevant files _No response_...
This PR adds the NGSCheckMate tool to the pipeline. I find this an essential tool and part of my initial QC for all sequencing we perform. This tool takes a...