Commit fc4f6694 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Merge branch 'de-containerize' into 'develop'

De containerize

See merge request !62
parents fbf1a9f7 8d8b4556
Pipeline #7352 passed with stages
in 7 minutes and 3 seconds
......@@ -11,7 +11,6 @@
**Background**
* Add Nextflow Tower integration into CI (GHH's profile)
* Utilize BICF docker containers
* Update to be runnable on cloud
* Refactor configs
......
......@@ -22,7 +22,10 @@ Additionally, the pipeline is designed to work with Astrocyte Workflow System us
Cloud Compatibility
-------------------
This pipeline is also capable of being run on AWS. To do so:
This pipeline is also capable of being run on AWS.\
**NOTE: This pipeline has been reverted to a non-containerized version to work on Astrocyte. Tag `containerized` for the last working containerized version which will be compatible with AWS.**
To do so:
* Build a AWS batch queue and environment either manually or with [aws-cloudformantion](https://console.aws.amazon.com/cloudformation/home?#/stacks/new?stackName=Nextflow&templateURL=https://s3.amazonaws.com/aws-genomics-workflows/templates/nextflow/nextflow-aio.template.yaml)
* In the aws configs in `workflow/configs/`:
* Replace workDir with the S3 bucket generated
......
......@@ -78,6 +78,7 @@ process trackStart {
process checkDesignFile {
tag "${name}"
module 'python/3.6.1-2-anaconda'
input:
file check_designScript
......@@ -114,6 +115,7 @@ process checkDesignFile {
process untarBCL {
tag "${tar.simpleName}"
module 'pigz/2.4'
input:
file untarBCLScript
......@@ -140,6 +142,7 @@ process mkfastq {
tag "${bcl.simpleName}"
publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
module 'cellranger/3.1.0:bcl2fastq/2.19.1'
input:
file versions_cellrangerScript
......@@ -202,6 +205,7 @@ if (bclCount.value == 1) {
process fastqc {
tag "${bcl}"
module 'fastqc/0.11.5:parallel'
input:
file fastqcScript
......@@ -229,6 +233,7 @@ process fastqc {
process versions {
tag "${name}"
module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
input:
file versionsScript
......@@ -261,6 +266,7 @@ process multiqc {
tag "${name}"
publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}"
module 'multiqc/1.7'
input:
file multiqcConf
......@@ -276,8 +282,8 @@ process multiqc {
hostname
ulimit -u 16384
ulimit -a
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
#export LC_ALL=C.UTF-8
#export LANG=C.UTF-8
multiqc -c ${multiqcConf} .
"""
......
......@@ -22,32 +22,6 @@ profiles {
}
}
process {
withName:checkDesignFile {
container = 'docker://bicf/python3:2.0.0'
}
withName:untarBCL {
container = 'docker://bicf/bicfbase:2.0.0'
}
withName:mkfastq {
container = 'docker://bicf/cellranger3.1.0:2.0.0'
}
withName:fastqc {
container = 'docker://bicf/fastqc:2.0.0'
}
withName:versions {
container = 'docker://bicf/python3:2.0.0'
}
withName:multiqc {
container = 'docker://bicf/multiqc:2.0.0'
}
}
singularity {
enabled = true
cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
}
trace {
enabled = true
file = 'pipeline_trace.txt'
......
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