These are chat archives for nextflow-io/nextflow
file 'sample.vcf*' into variants_ch
file subdir into variants_ch(a bit clunky)
file "sample.vcf*" into variants_chgives me input files
sample.vcf.idx1, which is why I didn't go for using glob, although that is much more clean.
file "sample.vcf*" into variants_ch, but as I mentioned above, I can't quite make it work.
I have one way that works. First the process that outputs the channel states:
output: file "sample.vcf*" into variants_ch
And then the process that takes the channel as input states:
input: file vcf from variants_ch
vcfis an array of files.
Although my original syntax is a bit cumbersome it seems to be the best solution. That is, in one process:
output: set file('sample.vcf'), file('sample.vcf.idx') into variants_ch
And then the subsequent process:
input: set file(vcf), file(idx) from variants_ch
Hi all. I've got a weird problem running Nextflow on MacOS X. Previously this was not a problem
I get the error
.command.stub: line 84: cannot create temp file for here-document: No space left on device
However df -h says
Filesystem Size Used Avail Capacity iused ifree %iused Mounted on /dev/disk1s1 466Gi 352Gi 111Gi 77% 2482701 9223372036852293106 0% / devfs 231Ki 231Ki 0Bi 100% 798 0 100% /dev /dev/disk1s4 466Gi 2.0Gi 111Gi 2% 2 9223372036854775805 0% /private/var/vm map -hosts 0Bi 0Bi 0Bi 100% 0 0 100% /net map auto_home 0Bi 0Bi 0Bi 100% 0 0 100% /home drivefs 466Gi 358Gi 108Gi 77% 18446744069414590987 4294967295 276728833924611296% /Volumes/GoogleDrive
root partition has space and I can create large files on /tmp no problem. I've asked around the office and I've drawn a blank so wondered if the 'hive mind' might be able to help
IFS=' ' read -a val <<< "$nxf_pstat_ret"; unset IFS