Use relative paths for inputs to make the training portable #438
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The training encoded an absolute path in the samplesheet. This broke the training when ran on a devcontainer. Importantly, Gitpod will be deprecating their custom format in April 2025 and using devcontainers so even if we don't merge this PR it will help indicate what we need to change.
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hello-nextflow/hello-config/main.nf
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| reads_ch = Channel.fromPath(params.reads_bam) | ||
| .splitText() | ||
| .map { it.trim() } |
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Annoyingly, we need a trim() in here to make it work. I'm not sure why we need this, but this is the simplest fix I can find.
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@adamrtalbot Can this be replaced by a .splitCsv() . From what I recall it doesn't need the trim.
Also, if we need to keep the it.trim() we are moving away from using the implicit it variable and should instead used named variables in our closures. It's much less confusing to newbies and will become mandatory in a future nextflow version according to Ben.
| reads_ch = Channel.fromPath(params.reads_bam) | ||
| .splitText() { bamPath -> file(bamPath.trim()) } |
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Does anyone know if there's a better way of doing this? Without the map nothing works 😠
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This is the equivalent splitCsv():
reads_ch = Channel.fromPath(params.reads_bam)
.splitCsv()
.map { bamPath -> file(bamPath[0]) }I think it looks nicer
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Yeah. I like that version a lot. It's a lot easier to follow.
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One thing we should keep in mind is that, at least for now, it's the same cloud environment for all training materials. We set a default start working directory based on our preferences at the time, but we should use absolute paths in some places to make sure people will be at the right place according to what training they're doing. |
Use splitCsv to parse the sample_bams samplesheet, which means we do not need to strip the newline characters from the file paths and can use relative paths.
adamrtalbot
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| /data/bam/reads_mother.bam | ||
| /data/bam/reads_father.bam | ||
| /data/bam/reads_son.bam |
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| /data/bam/reads_mother.bam | |
| /data/bam/reads_father.bam | |
| /data/bam/reads_son.bam | |
| ./data/bam/reads_mother.bam | |
| ./data/bam/reads_father.bam | |
| ./data/bam/reads_son.bam |
| ``` | ||
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| This should show `/workspaces/training/hello-nextflow`. The important point is the `hello-nextflow` is the final path. |
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| This should show `/workspaces/training/hello-nextflow`. The important point is the `hello-nextflow` is the final path. | |
| This should show `/workspaces/hello-nextflow`. The important point is the `hello-nextflow` is the final path. |
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See #462 for simpler short-term workaround |
The training encoded an absolute path in the samplesheet. This broke the
training when ran on a devcontainer. Importantly, Gitpod will be
deprecating their custom format in April 2025 and using devcontainers
so even if we don't merge this PR it will help indicate what we need to
change.