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This code
```console
nextflow run fmalmeida/ngs-preprocess -r dev -latest -profile docker --sra_ids "./input/sra_ids.txt" --output illumina_single --shortreads_type "single" --fastp_addit…
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Hi,
When I try to use fastqs from dorado --emit_fastq, nanoplexer spits out the wrong format for demultiplexed fastqs where it is missing the name row.
Do you know what the cause of that is? It…
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Hello!!
I am running args_oap on fastq files and in stage one I am getting the error as:
![image (1)](https://github.com/xinehc/args_oap/assets/114662100/559e0f65-b7d0-4678-b4e7-47d5d0fe4772)
…
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Ontology explorer:
```mermaid
graph TD;
Object--WITH_EXTENSION-->Fastq
Object--WITH_EXTENSION-->Ubam
Object--WITH_EXTENSION-->Gvcf
Fastq--CONTAINS_MATEPAIR-->PairedEndFastq
```
Where `WITH` and `CON…
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### Description of bug
(bio) zhisong@zhisongs-MacBook-Air spades % bin/spades.py -s ../accuvirnew/bad_nano/hiv_50_2k.fastq -o testfasta --isolate
== Error == /Users/zhisong/Desktop/accuvirnew/b…
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singularity exec -B databases/:/mnt/databases -B .:/mnt/host metapro_v3.0.1.sif python3 /pipeline/MetaPro.py -c /mnt/host/Config.ini -1 /mnt/host/forward.fastq -2 /mnt/host/reverse.fastq -o /mnt/host/…
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Hi,I have encountered an issue while trying to use the single_file and get_sample_map functions from the SGVFinder2 module. When I attempt to run my script, I receive the following error message:Trace…
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## Bug report
When using the publishDir directive to send outputs to an s3 location, it looks like Nextflow creates a zero-sized object with a key ending in a slash at the publishDir location. Whi…
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# Issue Report
## Please describe the issue:
Hi,
in version 0.7.2, `dorado demux` outputs all barcodes in the given kit in fastq format (`--emit-fastq`) even if the barcode is not listed in the …
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I am attempting to convert my fasta files to fastq using the command:
seq -F contig.2.fasta > contig.2.fq
but I keep getting:
seq: invalid option -- F