options(warn = 2)
in R, or use strict
in Perl?
script
/shell
section but a change to the set(…)
spec for a channel
strict
flag at some point
nextflow self-update
using sudo, as I have it in /opt/
. It appears that also changes stuff in ~/.nextflow
, for example the framkework dir. This is then owned by root and nextflow console
does not work anymore. Easy to fix, but is it supposed to work like that?
nextflow
launcher script in /usr/local/bin
storeDir
really discouraged?
cache 'deep'
buffer
operator so that the opening and closing criteria could access to the buffers content as well?
#!/bin/bash -ue
awk '{if($2 == 4){ print "@" $1 "
" $10 "
+
" $11 }}' reads.umi.cut.rrna.sam > reads.umi.clean.fq
#!/bin/bash -ue
awk '{if($2 == 4){ print "@" $1 "
" $10 "
+
" $11 }}' reads.umi.cut.rrna.sam > reads.umi.clean.fq
process extrac_unaligned_rrna {
input:
file "reads.umi.cut.rrna.sam" from rrna
output:
file "reads.umi.clean.fq" into clean
shell:
'''awk '{if($2 == 4){ print "@" $1 "\n" $10 "\n+\n" $11 }}' reads.umi.cut.rrna.sam > reads.umi.clean.fq'''
}
Command error:
awk: cmd. line:1: {if($2 == 4){ print "@" $1 "
awk: cmd. line:1: ^ unterminated string
awk: cmd. line:1: {if($2 == 4){ print "@" $1 "
awk: cmd. line:1: ^ syntax error
I don't use shell:
blocs, but from the Nextflow documentation
https://www.nextflow.io/docs/latest/process.html#shell
there is a note about
Shell script definition requires the use of single-quote ' delimited strings. When using double-quote " delimited strings, dollar variables are interpreted as Nextflow variables as usual. See String interpolation.
nextflow run -process.executor slurm ...
NXF_EXECUTOR
with the default executor you want to use