Commit f21d0604 authored by Brandi Cantarel's avatar Brandi Cantarel
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Merge branch 'singularity' into 'master'

Singularity

See merge request !10
parents 6d3d64fe c19cb854
Pipeline #10025 failed with stage
in 78 minutes and 18 seconds
# Gitlab CI Script for astrocyte/rnaseq
# Brandi L. Cantarel - 2017
variables:
GIT_SUBMODULE_STRATEGY: recursive
before_script:
- module load nextflow/0.31.0
- git submodule sync --recursive
- git submodule update --init --recursive
- module load nextflow/20.01.0
- module load singularity/3.0.2
stages:
- integration
......@@ -12,13 +14,13 @@ stages:
test_human:
stage: integration
script:
- nextflow run -with-dag flowchart.png -with-timeline human_timeline.html -with-report human_report.html workflow/main.nf --design /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/design.rnaseq.txt --input /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --output human_output
- nextflow run -c nextflow.config -with-dag flowchart.png -with-timeline human_timeline.html -with-report human_report.html workflow/main.nf --design /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/design.rnaseq.txt --input /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --output human_output
artifacts:
expire_in: 2 days
test_mouse:
stage: integration
script:
- nextflow run -with-dag flowchart.png -with-timeline mouse_timeline.html -with-report mouse_report.html workflow/main.nf --input /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --design /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/mouse/GRCm38 --markdups null --output mouse_output
- nextflow run -c nextflow.config -with-dag flowchart.png -with-timeline mouse_timeline.html -with-report mouse_report.html workflow/main.nf --input /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --design /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/mouse/GRCm38 --markdups null --output mouse_output
artifacts:
expire_in: 2 days
[submodule "workflow/process_scripts"]
path = workflow/process_scripts
url = git@git.biohpc.swmed.edu:ngsclialab/process_scripts.git
## RNASeq Analysis Worklow
# RNASeq Analysis Worklow
This workflow can be run in with the whole genome, or with a specific list of genes of interest.
## Initiate Nextflow Workflows
### Required Tools
This pipeline uses [Nextflow](https://www.nextflow.io/docs/latest/index.html), a bioinformatics workflow tool and [Singularity](https://sylabs.io/docs/), a containerization tool.
Make sure both tools rae installed before running this pipeline. If running on a HPC cluster then load required modules.
```
module load nextflow/20.01.0 singularity/3.5.3
```
### RNA Design File
The design file must named design.txt and be in tab seperated format for the workflows. All RNA workflows can be run usin the same design file format. You can run in single-end mode with blank cells in the FqR2 column.
| SampleID | CaseID | FqR1 | FqR2 |
|---|---|---|---|
| Sample1 | Fam1 | Sample1.R1.fastq.gz | Sample1.R2.fastq.gz |
| Sample2 | Fam1 | Sample2.R1.fastq.gz | Sample2.R2.fastq.gz |
| Sample3 | Fam2 | Sample3.R1.fastq.gz | Sample3.R2.fastq.gz |
| Sample4 | Fam2 | Sample4.R1.fastq.gz | Sample4.R2.fastq.gz |
### RNA Parameters
* **--input**
* directory containing the design file and fastq files
* default is set to *'${basedir}/fastq'*
* eg: **--input '/project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/fastq'**
* **--output**
* directory for the analysis output
* default is set to *'${basedir}/analysis'*
* eg: **--output '${basedir}/output'**
* **--genome**
* directory containing all reference files for the various tools. This includes the genome.fa, gencode.gtf, genenames.txt, ect.
* default is set for use on UTSW BioHPC.
* eg: **--genome '/project/shared/bicf_workflow_ref/human/grch38_cloud/rnaref'**
* **--stranded**
* option for -s flag in featurecount used in geneabundance calculations
* default is set to *'0'*
* eg: **--stranded '0'**
* **--pairs**
* select either 'pe' (paired-end) or 'se' (single-end) based on read inputs. Select 'pe' when both R1 and R2 are present. If only R1, then select 'se'.
* default is set to *'pe'*
* eg: **--pairs 'pe'**
* **--align**
* select the algorithm/tool for alignment from 'hisat' or 'star'
* default is set to *'hisat'*
* eg: **--align 'hisat'**
* **--markdups**
* select either picard (Mark Duplicates) or null (do not Mark Duplicates)
* default is set to *'picard'*
* eg: **--align 'picard'**
### RNA Run Workflow Testing
Human PE
```
module load nextflow/20.01.0 singularity/3.5.3
base=$repoClonedDirectory
datadir='/project/shared/bicf_workflow_ref/workflow_testdata/rnaseq'
nextflow -C ${base}/nextflow.config run ${base}/workflow/main.nf --design ${datadir}/design.rnaseq.txt --input ${datadir} --output analysis
```
module load nextflow
nextflow run workflow/main.nf
Mouse SE
```
module load nextflow/20.01.0 singularity/3.5.3
base=$repoClonedDirectory
datadir='/project/shared/bicf_workflow_ref/workflow_testdata/rnaseq'
nextflow -C ${base}/nextflow.config run -with-dag flowchart.png -with-timeline mouse_timeline.html -with-report mouse_report.html ${base}/workflow/main.nf --design ${datadir}/mouse_se.design.txt --input ${datadir} --pairs se --output analysis
```
......@@ -161,6 +161,7 @@ workflow_parameters:
- [ '/project/shared/bicf_workflow_ref/human/GRCh38', 'Human GRCh38']
- [ '/project/shared/bicf_workflow_ref/human/GRCh37', 'Human GRCh37']
- [ '/project/shared/bicf_workflow_ref/mouse/GRCm38', 'Mouse GRCm38']
- [ '/project/shared/bicf_workflow_ref/mouse/GRCm39', 'Mouse GRCm39']
required: true
description: |
Reference genome for alignment
......
......@@ -6,32 +6,41 @@ process {
clusterOptions = '--hold --no-kill'
queue = '128GB,256GB,256GBv1'
withLabel: trim {
container = 'trim_galore.sif'
container = 'goalconsortium/trim_galore:1.0.9'
}
withLabel: dnaalign {
container = 'dna_alignment.sif'
withLabel: abra2 {
container = 'goalconsortium/abra2:1.0.9'
}
withLabel: profiling_qc {
container = 'profiling_qc.sif'
container = 'goalconsortium/profiling_qc:1.0.9'
}
withLabel: dnaalign {
container = 'goalconsortium/dna_alignment:1.0.9'
}
withLabel: variantcalling {
container = 'goalconsortium/variantcalling:1.0.9'
}
withLabel: structuralvariant {
container = 'goalconsortium/structuralvariant:1.1.2'
}
withLabel: starfusion {
container = 'starfusion.sif'
container = 'goalconsortium/starfusion:1.0.9'
}
withLabel: ralign {
container = 'rna_alignment.sif'
container = 'goalconsortium/rna_alignment:1.0.9'
}
withLabel: geneabund {
container = 'rna_gene_abundance.sif'
container = 'goalconsortium/rna_gene_abundance:1.1.3'
}
withLabel: rnaseqstat {
container = 'rnaseq_dea.sif'
container = 'goalconsortium/rna_statanal:1.1.4'
}
}
singularity {
enabled = true
runOptions='--no-home --cleanenv'
cacheDir = '/project/shared/bicf_workflow_ref/seqprg/singularity/'
singularity.cacheDir="$PWD"
}
trace {
......@@ -57,9 +66,9 @@ env {
}
manifest {
homePage = 'https://git.biohpc.swmed.edu/ngsclialab/school'
description = 'School is a collection of genomics analysis workflows that are used for detecting single nucleotide variants (SNVs), insertions/deletions (indels), copy number variants (CNVs) and translocations from RNA and DNA sequencing. These workflows have been validated in a CLIA laboratory at UTSW'
homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq'
description = 'RNA sequencing gene abundance analysis'
mainScript = 'rna.nf'
version = '1.0.0'
nextflowVersion = '>=0.31.0'
nextflowVersion = '>=20.01.0'
}
#!/bin/bash
module load nextflow/20.01.0 singularity/3.5.3
base='/project/BICF/BICF_Core/s166458/rnaseq_astrocyte'
datadir='/project/shared/bicf_workflow_ref/workflow_testdata/rnaseq'
nextflow -C ${base}/nextflow.config run ${base}/workflow/main.nf --design ${datadir}/design.rnaseq.txt --input ${datadir} --output analysis
#!/bin/bash
module load nextflow/20.01.0 singularity/3.5.3
base='/project/BICF/BICF_Core/s166458/rnaseq_astrocyte'
datadir='/project/shared/bicf_workflow_ref/workflow_testdata/rnaseq'
nextflow -C ${base}/nextflow.config run -with-dag flowchart.png -with-timeline mouse_timeline.html -with-report mouse_report.html ${base}/workflow/main.nf --design ${datadir}/mouse_se.design.txt --input ${datadir} --pairs se --output analysis
#!/bin/bash
baseDir="`dirname \"$0\"`"
cd ${baseDir}/mouse_se_test/
sbatch -p 32GB,super run_test.sh
cd ${baseDir}/human_pe_test/
sbatch -p 32GB,super run_test.sh
Subproject commit 8706de703b8b5933f89651e5be0312af96cddb7c
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