I'm remarkably still struggling with some basic Nextflow
concepts. I'm simply trying to collect all pairs of .cram
and .crai
files from a directory using Channel.fromFilePairs(...)
, but I get no output when I try to view()
the Channel
.
Question: Why does my Channel.fromFilePairs(...)
command not return file pairs, but I get a list of files when using Channel.fromPath(...)
?
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 {
/*
* Channel.fromPath returns the expected files and prints them to
* terminal.
*/
Channel.fromPath('/path/to/adsp/cram/snd10000/A-CUHS-CU000*.cram')
| view()
/*
* Channel.fromFilePairs does not print anything to terminal.
*/
Channel.fromFilePairs('/path/to/adsp/cram/snd10000/A-CUHS-CU000*.{cram,crai}')
| view()
}
Output (note, no file tuples/pairs)
N E X T F L O W ~ version 21.04.3
Launching `pairs.nf` [pensive_plateau] - revision: f917a5c41b
/path/to/adsp/cram/snd10000/A-CUHS-CU000563-BL-COL-47451BL1_vcpa1.1.cram.crai
/path/to/adsp/cram/snd10000/A-CUHS-CU000387-BL-COL-38200BL2_vcpa1.1.cram.crai
/path/to/adsp/cram/snd10000/A-CUHS-CU000018-BL-COL-46250BL1_vcpa1.1.cram.crai
/path/to/adsp/cram/snd10000/A-CUHS-CU000169-BL-COL-57413BL1_vcpa1.1.cram
/path/to/adsp/cram/snd10000/A-CUHS-CU000563-BL-COL-47451BL1_vcpa1.1.cram
/path/to/adsp/cram/snd10000/A-CUHS-CU000387-BL-COL-38200BL2_vcpa1.1.cram
/path/to/adsp/cram/snd10000/A-CUHS-CU000194-BL-COL-38470BL1_vcpa1.1.cram
/path/to/adsp/cram/snd10000/A-CUHS-CU000194-BL-COL-38470BL1_vcpa1.1.cram.crai
/path/to/adsp/cram/snd10000/A-CUHS-CU000169-BL-COL-57413BL1_vcpa1.1.cram.crai
/path/to/adsp/cram/snd10000/A-CUHS-CU000018-BL-COL-46250BL1_vcpa1.1.cram