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Commit 57834f48 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Add finalize execution run and add new references using bag

parent beecb815
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2 merge requests!58Develop,!56Resolve "Detect error in inferMetadata for tracking"
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README.md
+ 2
− 2
View file @ 57834f48
......@@ -40,7 +40,7 @@ To Run:
* `--refMoVersion` mouse reference version ***(optional, default = 38.p6.vM22)***
* `--refHuVersion` human reference version ***(optional, default = 38.p12.v31)***
* `--refERCCVersion` human reference version ***(optional, default = 92)***
* `--upload` option to not upload output back to the data-hub ***(optional, default = true)***
* `--upload` option to not upload output back to the data-hub ***(optional, default = false)***
* **true** = upload outputs to the data-hub
* **false** = do *NOT* upload outputs to the data-hub
* `-profile` config profile to use ***(optional)***:
......@@ -69,7 +69,7 @@ To Run:
* eg: `--speciesForce 'Mus musculus'`
* Tracking parameters ([Tracking Site](http://bicf.pipeline.tracker.s3-website-us-east-1.amazonaws.com/)):
* `--ci` boolean (default = false)
* `--dev` boolean (default = false)
* `--dev` boolean (default = true)
FULL EXAMPLE:
-------------
......
workflow/conf/aws.config
+ 30
− 22
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......@@ -16,91 +16,99 @@ process {
cpus = 1
memory = '1 GB'
withName: trackStart {
withName:trackStart {
cpus = 1
memory = '1 GB'
}
withName: getBag {
withName:getBag {
cpus = 1
memory = '1 GB'
}
withName: getData {
withName:getData {
cpus = 1
memory = '1 GB'
}
withName: parseMetadata {
withName:parseMetadata {
cpus = 15
memory = '1 GB'
}
withName: trimData {
withName:trimData {
cpus = 20
memory = '2 GB'
}
withName: getRefInfer {
withName:getRefInfer {
cpus = 1
memory = '1 GB'
}
withName: downsampleData {
withName:downsampleData {
cpus = 1
memory = '1 GB'
}
withName: alignSampleData {
withName:alignSampleData {
cpus = 50
memory = '5 GB'
}
withName: inferMetadata {
withName:inferMetadata {
cpus = 5
memory = '1 GB'
}
withName: getRef {
withName:checkMetadata {
cpus = 1
memory = '1 GB'
}
withName: alignData {
withName:getRef {
cpus = 1
memory = '1 GB'
}
withName:alignData {
cpus = 50
memory = '10 GB'
}
withName: dedupData {
withName:dedupData {
cpus = 5
memory = '20 GB'
}
withName: countData {
withName:countData {
cpus = 2
memory = '5 GB'
}
withName: makeBigWig {
withName:makeBigWig {
cpus = 15
memory = '5 GB'
}
withName: fastqc {
withName:fastqc {
cpus = 1
memory = '1 GB'
}
withName: dataQC {
withName:dataQC {
cpus = 15
memory = '2 GB'
}
withName: aggrQC {
withName:aggrQC {
cpus = 2
memory = '1 GB'
}
withName: uploadInputBag {
withName:uploadInputBag {
cpus = 1
memory = '1 GB'
}
withName:uploadExecutionRun {
cpus = 1
memory = '1 GB'
}
withName: uploadExecutionRun {
withName:uploadQC {
cpus = 1
memory = '1 GB'
}
withName: uploadQC {
withName:uploadProcessedFile {
cpus = 1
memory = '1 GB'
}
withName: uploadProcessedFile {
withName:uploadOutputBag {
cpus = 1
memory = '1 GB'
}
withName: uploadOutputBag {
withName:finalizeExecutionRun {
cpus = 1
memory = '1 GB'
}
......
workflow/conf/biohpc.config
+ 28
− 22
View file @ 57834f48
......@@ -7,70 +7,76 @@ process {
queue = 'super'
clusterOptions = '--hold'
withName: trackStart {
withName:trackStart {
executor = 'local'
}
withName: getBag {
withName:getBag {
executor = 'local'
}
withName: getData {
withName:getData {
queue = 'super'
}
withName: parseMetadata {
withName:parseMetadata {
executor = 'local'
}
withName: trimData {
withName:trimData {
queue = 'super'
}
withName: getRefInfer {
withName:getRefInfer {
queue = 'super'
}
withName: downsampleData {
withName:downsampleData {
executor = 'local'
}
withName: alignSampleData {
withName:alignSampleData {
queue = 'super'
}
withName: inferMetadata {
withName:inferMetadata {
queue = 'super'
}
withName: getRef {
withName:checkMetadata {
executor = 'local'
}
withName:getRef {
queue = 'super'
}
withName: alignData {
withName:alignData {
queue = '256GB,256GBv1'
}
withName: dedupData {
withName:dedupData {
queue = 'super'
}
withName: countData {
withName:countData {
queue = 'super'
}
withName: makeBigWig {
withName:makeBigWig {
queue = 'super'
}
withName: fastqc {
withName:fastqc {
queue = 'super'
}
withName: dataQC {
withName:dataQC {
queue = 'super'
}
withName: aggrQC {
withName:aggrQC {
executor = 'local'
}
withName:uploadInputBag {
executor = 'local'
}
withName: uploadInputBag {
withName:uploadExecutionRun {
executor = 'local'
}
withName: uploadExecutionRun {
withName:uploadQC {
executor = 'local'
}
withName: uploadQC {
withName:uploadProcessedFile {
executor = 'local'
}
withName: uploadProcessedFile {
withName:uploadOutputBag {
executor = 'local'
}
withName: uploadOutputBag {
withName:finalizeExecutionRun {
executor = 'local'
}
}
......
workflow/nextflow.config
+ 21
− 15
View file @ 57834f48
......@@ -25,46 +25,49 @@ process {
withName:getData {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
withName: parseMetadata {
withName:parseMetadata {
container = 'gudmaprbk/python3:1.0.0'
}
withName: trimData {
withName:trimData {
container = 'gudmaprbk/trimgalore0.6.5:1.0.0'
}
withName: getRefInfer {
withName:getRefInfer {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
withName: downsampleData {
withName:downsampleData {
container = 'gudmaprbk/seqtk1.3:1.0.0'
}
withName: alignSampleData {
withName:alignSampleData {
container = 'gudmaprbk/hisat2.2.1:1.0.0'
}
withName: inferMetadata {
withName:inferMetadata {
container = 'gudmaprbk/rseqc4.0.0:1.0.0'
}
withName: getRef {
withName:checkMetadata {
container = 'gudmaprbk/gudmap-rbk_base:1.0.0'
}
withName:getRef {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
withName: alignData {
withName:alignData {
container = 'gudmaprbk/hisat2.2.1:1.0.0'
}
withName: dedupData {
withName:dedupData {
container = 'gudmaprbk/picard2.23.9:1.0.0'
}
withName: countData {
withName:countData {
container = 'gudmaprbk/subread2.0.1:1.0.0'
}
withName: makeBigWig {
withName:makeBigWig {
container = 'gudmaprbk/deeptools3.5.0:1.0.0'
}
withName: fastqc {
withName:fastqc {
container = 'gudmaprbk/fastqc0.11.9:1.0.0'
}
withName: dataQC {
withName:dataQC {
container = 'gudmaprbk/rseqc4.0.0:1.0.0'
}
withName: aggrQC {
withName:aggrQC {
container = 'gudmaprbk/multiqc1.9:1.0.0'
}
withName:uploadInputBag {
......@@ -82,6 +85,9 @@ process {
withName:uploadOutputBag {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
withName:finalizeExecutionRun {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
}
trace {
......@@ -110,6 +116,6 @@ manifest {
homePage = 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq'
description = 'This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub.'
mainScript = 'rna-seq.nf'
version = 'v0.0.4_indev'
version = 'v0.1.0'
nextflowVersion = '>=19.09.0'
}
workflow/rna-seq.nf
+ 450
− 212
View file @ 57834f48
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