Is there a way to increase the width of the nextflow stdout? I have looked through the documentation, but I can't see anything. I realise this might be a parameter of the bash environment instead, but also couldn't find a way to change this.
In this instance, there is some information missing from tag{ sampleID+"-"+MapperVal } in
all the Mapping jobs.
executor > local (1), pbspro (9)
[e0/c2b561] process > GFF_Check (1) [100%] 1 of 1 ✔
[fe/0aa2b0] process > Mapping (Merged_Barcode09-m... [ 0%] 0 of 9
[- ] process > FormatBams -
[- ] process > IsoQuant -
[- ] process > ESPRESSO_S -
Using a modified version of helloWorld as an example, where I have made the tag extremely long:
#!/usr/bin/env nextflow
nextflow.enable.dsl=2
process sayHelloWithQuiteALongName {
input:
val x
tag "$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x$x"
output:
stdout
script:
"""
echo '$x world!'
"""
}
workflow {
Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHelloWithQuiteALongName | view
}
Regular parameters trims the line when it gets too long:
nextflow run hw/main.nf
nextflow run hw/main.nf -ansi-log true
N E X T F L O W ~ version 21.10.6
Launching `hw/main.nf` [deadly_pasteur] - revision: af5625b97b
executor > local (4)
[80/c3d0ae] process > sayHelloWithQuiteALongName (BonjourBonjourBonjourBonjourBo... [100%] 4 of 4 ✔
Hola world!
Hello world!
Ciao world!
Bonjour world!
Turning off ansi logging:
nextflow run hw/main.nf -ansi-log false
N E X T F L O W ~ version 21.10.6
Launching `hw/main.nf` [big_agnesi] - revision: af5625b97b
[e7/acaa39] Submitted process > sayHelloWithQuiteALongName (BonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjourBonjour)
[f7/33263c] Submitted process > sayHelloWithQuiteALongName (CiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiaoCiao)
[c9/4f9251] Submitted process > sayHelloWithQuiteALongName (HelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHelloHello)
[05/eeff7a] Submitted process > sayHelloWithQuiteALongName (HolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHolaHola)
Bonjour world!
Ciao world!
Hello world!
Hola world!
A downside is that you don't have each job concatenated into a single line.