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Update [fastqc_per_base_sequence_quality_dropoff.py](https://github.com/aomlomics/tourmaline/blob/develop/scripts/fastqc_per_base_sequence_quality_dropoff.py) to work with fastq_summary.qzv output
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### Description of the bug
- If there are two FastQC sections displaying the read stats before/after preprocessing, then why are there six samples in each FastQC diagram? I'm expecting 3 samples, a…
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Hello,
I've been working with CARLIN data using the prior MATLAB pipeline and was very excited to migrate to this improved snakemake_DARLIN implementation for batch submissions. I would like to run t…
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Nextflow 22.04 brings with it two new features which should give much cleaner syntax for collecting tool versions: channel topics using `topic` (see https://github.com/nf-core/modules/issues/4517) and…
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Hi Felix,
I am sorry to trouble you. I’m having some trouble with the FastQC report and would like to ask you.
1. According to the “Per base sequence content”, should I clip the first 6 bp for go…
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## Versions
`snakemake` version 8.10.7
`snakemake-executor-plugin-slurm` version 0.4.4
`snakemake-executor-plugin-slurm-jobstep` version 0.2.1
## The problem
I am working on getting `snakemake`…
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Hi! By running the following command:
nextflow run mop_preprocess.nf -with-docker -bg --fast5 " " --fastq files "/home/MOP2/mop_preprocess/fastq/ " --reference "Homo_sapiens.GRCh37.cdna.fa" --annot…
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Starting an issue to keep track of this limitation in our current implementations of deduplication and duplicate statistics.
Currently the `CLUMPIFY_PAIRED` process has the comment flag "NB: Will N…
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Hi
I am having issues running the fastqc_run_parallel.pbs script on Gadi, the job fails when queued and returns the following error. I am working on Ubuntu 22.04.4 LTS.
sed: can't read ./Inputs/fa…
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# Quality Control
I generate raw-samples.txt which has the sample_name, R1 and R2 as columns.
```
# Get R1 and R2
ls 00-RAW/ | tr " " "\n" | paste - - > doc/tmp.r1_r2.txt
# Get sample names
…