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A pipeline to investigate horizontal gene transfer from NGS data

Home Page: https://nf-co.re/hgtseq

License: MIT License

HTML 1.64% Nextflow 60.85% Groovy 31.31% Python 6.20%
nextflow nf-core pipeline workflow horizontal-gene-transfer ngs taxonomies bwa-mem bwa-mem2 fastqc

hgtseq's People

Contributors

carpanz avatar ewels avatar lescai avatar maxulysse avatar nf-core-bot avatar

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Forkers

yuzhenpeng zhypc carpanz biofriends latchbio-nfcore

hgtseq's Issues

samtools stats output only one bam file

Description of the bug

inspecting the multiQC report, all samtools statistics only report one sample called "sorted".
this bam file and its corresponding bai are present in the results alignment folder, along with all the expected bam files (not their .bai) of all input samples.
something might be wrong in the channel leading up to the samtools stats, and might refer to the module that's publishing in the same folder of the alignments.

Command used and terminal output

No response

Relevant files

No response

System information

version 22.04.0, build 5697
executor slurm on CentOS

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