Commit 75e3b284 authored by Venkat Malladi's avatar Venkat Malladi

Merge branch '18-ErrorStratagy' into 'master'

add in error strategy

Closes #18

See merge request !8
parents 7c2ae90f 7ff15f77
Pipeline #4831 passed with stage
in 109 minutes and 40 seconds
......@@ -74,6 +74,7 @@ if( ! read ) { error "Didn't match any input files with entries in the design fi
// Trim raw reads using trimgalore
process trim {
errorStrategy 'ignore'
input:
set pair_id, file(read1), file(read2) from read
......@@ -94,6 +95,7 @@ process trim {
// Alignment stats with samtools
process starfusion {
errorStrategy 'ignore'
publishDir "$params.output", mode: 'copy'
input:
......@@ -112,6 +114,7 @@ process starfusion {
}
process align {
errorStrategy 'ignore'
publishDir "$params.output", mode: 'copy'
input:
......@@ -129,6 +132,7 @@ process align {
}
process alignqc {
errorStrategy 'ignore'
publishDir "$params.output", mode: 'copy'
input:
......@@ -184,6 +188,7 @@ process markdups {
// Assemble transcripts with stringtie
process geneabund {
errorStrategy 'ignore'
publishDir "$params.output", mode: 'copy'
input:
......@@ -202,6 +207,7 @@ process geneabund {
}
process statanal {
errorStrategy 'ignore'
publishDir "$params.output", mode: 'copy'
input:
......@@ -226,6 +232,7 @@ process statanal {
}
process gatkbam {
errorStrategy 'ignore'
publishDir "$params.output", mode: 'copy'
input:
......
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