Container for FASTQSCREEN_FASTQSCREEN should include bismark
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@fbnrst is already working on this.
Since Jul 5, 2025.
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Description
Have you checked the docs?
Description of the bug
Fastq-screen can also be used for bisulfite sequencing analysis. For bisulfite sequencing, Bismark is a requirement, but Bismark is not present in the current container:
https://github.com/nf-core/modules/blob/fac12e7a9e255c22265ff84b09f628e03c7b96fe/modules/nf-core/fastqscreen/fastqscreen/main.nf#L6-L8
I did run into this, when I supplied the --bismark argument to FASTQSCREEN_FASTQSCREEN via ext.args.
Command used and terminal output
❯ singularity shell https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0
Singularity> bismark
bash: bismark: command not found
Relevant files
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System information
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