Commit 9d33dcb0 authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Execute pipeline with singularity

parent 2d250508
......@@ -2,10 +2,9 @@
params.location = 's3://lj-nf-fastq-testdata/data/*.fastq.gz'
params.publish = 's3://lj-nf-fastq-testdata/results/'
Channel.fromPath(params.location).into{ch_fastqs1}
Channel.fromPath(params.location).set{ch_fastqs1}
process run_fastqc {
publishDir params.publish
input:
......@@ -22,7 +21,6 @@ process run_fastqc {
}
process run_multiqc {
publishDir params.publish
input:
......
process {
executor = "sge"
withName:run_fastqc {
container = "docker://quay.io/biocontainers/fastqc:0.11.7--5"
}
withName:run_multiqc {
container = "docker://quay.io/biocontainers/multiqc:1.6--py36h24bf2e0_0"
}
}
singularity {
enabled = true
}
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