Matthias De Smet

bclconvert module - Undetermined barcodes not shown

3

### Description of bug Bclconvert module is missing the section to visualise the top unknown barcodes ### File that triggers the error _No response_ ### MultiQC Error log _No response_

Backend request: Hashicorp Nomad

1

Hi, I was wondering if there's any interest to support a new backend for submitting jobs to a Hashicorp Nomad cluster? I suppose this will be fairly similar to the...

`--sam-append-comment` adds raw header as sam comment

3

Hi, I noticed a part of the fastq header is interpreted as a fastq comment on alignment. version: `2.4.5` command: `bowtie2 --local --fast-local -p 10 -x /Shared/references/Hsapiens/hg38-noalt/bowtie2/hg38-noalt.fa --sam-append-comment -1 fq_1.fastq...

Segmentation fault when aligning bam with multiprocessing

14

Hi, I'm trying to align some uBam files using Bowtie2 v2.2.4 with the following commands ``` bowtie2 -b sample_L2.unaligned.bam --preserve-tags --fast-local -x /references/Hsapiens/hg38/bowtie2/hg38 -p 4 bowtie2-align-s -b sample_L2.unaligned.bam --preserve-tags --fast-local...

Alignment from uBam drops tags with `--preserve-tags`

2

Hi, when testing the uBam alignment with the `--preserve-tags` flag, I noticed the the `@RG` header and the `RG` tag got left behind. Is this something that can be fixed?...

Issue querying db's made with latest cyvcf2

5

Hi @brentp, I've come across a weird issue. I've updated one of our bcbio installations, resulting in an environment with the latest vcf2db + cyvcf2=0.30.14. When I try to query...

Compute: HashiCorp Nomad

9

Hi, We'd like to use Funnel to schedule jobs on a HashiCorp Nomad cluster. Are there plans to support this? Or are there any resources available on how we could...

Allow Directory + String = File concatenation

1

Hi Would it be possible to allow user to create a `File` variable by concatenating `Directory` + `String` types? This would be useful to point to known files in a...