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Results tagged with nextflow
Search options questions only
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user 136
6
votes
1
answer
1k
views
Nextflow: dynamically setting resource directives for a process
To do this, I'd like to set the CPU and memory for a Nextflow process dynamically. … for two reasons:
To learn Nextflow better
Because the traces provided by Nextflow are super convenient (though I could get this information from SLURM, too). …
- 1,414
2
votes
1
answer
629
views
Nextflow: cannot get file pairs from Channel.fromFilePairs
I'm remarkably still struggling with some basic Nextflow concepts. … As far as I can tell, I'm following the same pattern from the following examples:
Nextflow fromFilePairs
.bam/.bai example (except without the extra code)
Code
nextflow.enable.dsl=2
workflow { …
- 1,414
2
votes
2
answers
2k
views
Nextflow: how to create many-to-many tuple for process
Using Nextflow, I need to submit x * y jobs where x is the number of input .bam files and y is the number of genome intervals (e.g., <chrom>:<start>-<end>). i.e., for every .bam file, submit a single job … Ultimate question: For each .bam file, how do I submit a single job for every defined genome interval using NextFlow? …
- 1,414
6
votes
2
answers
3k
views
Nextflow (DSL v2): how to best synchronize multiple outputs from a single process
Bonus question (may be worth a separate post): does Nextflow not stage files until the actual .bash script starts? … *
* Does Nextflow not stage files until the actual .bash script starts? …
- 1,414
3
votes
1
answer
732
views
Nextflow scheduler job doesn't end upon successful workflow completion
Bug fixed
This issue appears to have been fixed in latest Nextflow: https://github.com/nextflow-io/nextflow/issues/2693
I've been using Nextflow for various workflows on a cluster using the SLURM scheduler … I saw a post on the Nextflow GitHub where the original poster describes various acrobatics to get the parent job to exit cleanly, but this is something that Nextflow should handle. …
- 1,414
4
votes
1
answer
687
views
BWA mem | samtools view: Intermittent parsing error
It only seems to happen when the command runs within a Nextflow pipeline (though it seems unlikely that Nextflow has anything to do with it). … Nextflow process
Here's the Nextflow process I'm running (code credit to @Steve, though modified to handle .bam or .cram). …
- 1,414