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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: ...@@ -40,7 +40,7 @@ To Run:
* `--refMoVersion` mouse reference version ***(optional, default = 38.p6.vM22)*** * `--refMoVersion` mouse reference version ***(optional, default = 38.p6.vM22)***
* `--refHuVersion` human reference version ***(optional, default = 38.p12.v31)*** * `--refHuVersion` human reference version ***(optional, default = 38.p12.v31)***
* `--refERCCVersion` human reference version ***(optional, default = 92)*** * `--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 * **true** = upload outputs to the data-hub
* **false** = do *NOT* upload outputs to the data-hub * **false** = do *NOT* upload outputs to the data-hub
* `-profile` config profile to use ***(optional)***: * `-profile` config profile to use ***(optional)***:
...@@ -69,7 +69,7 @@ To Run: ...@@ -69,7 +69,7 @@ To Run:
* eg: `--speciesForce 'Mus musculus'` * eg: `--speciesForce 'Mus musculus'`
* Tracking parameters ([Tracking Site](http://bicf.pipeline.tracker.s3-website-us-east-1.amazonaws.com/)): * Tracking parameters ([Tracking Site](http://bicf.pipeline.tracker.s3-website-us-east-1.amazonaws.com/)):
* `--ci` boolean (default = false) * `--ci` boolean (default = false)
* `--dev` boolean (default = false) * `--dev` boolean (default = true)
FULL EXAMPLE: FULL EXAMPLE:
------------- -------------
......
workflow/conf/aws.config
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...@@ -16,91 +16,99 @@ process { ...@@ -16,91 +16,99 @@ process {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
withName: trackStart { withName:trackStart {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
} }
withName: getBag { withName:getBag {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
} }
withName: getData { withName:getData {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
} }
withName: parseMetadata { withName:parseMetadata {
cpus = 15 cpus = 15
memory = '1 GB' memory = '1 GB'
} }
withName: trimData { withName:trimData {
cpus = 20 cpus = 20
memory = '2 GB' memory = '2 GB'
} }
withName: getRefInfer { withName:getRefInfer {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
} }
withName: downsampleData { withName:downsampleData {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
} }
withName: alignSampleData { withName:alignSampleData {
cpus = 50 cpus = 50
memory = '5 GB' memory = '5 GB'
} }
withName: inferMetadata { withName:inferMetadata {
cpus = 5 cpus = 5
memory = '1 GB' memory = '1 GB'
} }
withName: getRef { withName:checkMetadata {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
} }
withName: alignData { withName:getRef {
cpus = 1
memory = '1 GB'
}
withName:alignData {
cpus = 50 cpus = 50
memory = '10 GB' memory = '10 GB'
} }
withName: dedupData { withName:dedupData {
cpus = 5 cpus = 5
memory = '20 GB' memory = '20 GB'
} }
withName: countData { withName:countData {
cpus = 2 cpus = 2
memory = '5 GB' memory = '5 GB'
} }
withName: makeBigWig { withName:makeBigWig {
cpus = 15 cpus = 15
memory = '5 GB' memory = '5 GB'
} }
withName: fastqc { withName:fastqc {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
} }
withName: dataQC { withName:dataQC {
cpus = 15 cpus = 15
memory = '2 GB' memory = '2 GB'
} }
withName: aggrQC { withName:aggrQC {
cpus = 2 cpus = 2
memory = '1 GB' memory = '1 GB'
} }
withName: uploadInputBag { withName:uploadInputBag {
cpus = 1
memory = '1 GB'
}
withName:uploadExecutionRun {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
} }
withName: uploadExecutionRun { withName:uploadQC {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
} }
withName: uploadQC { withName:uploadProcessedFile {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
} }
withName: uploadProcessedFile { withName:uploadOutputBag {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
} }
withName: uploadOutputBag { withName:finalizeExecutionRun {
cpus = 1 cpus = 1
memory = '1 GB' memory = '1 GB'
} }
......
workflow/conf/biohpc.config
+ 28
− 22
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...@@ -7,70 +7,76 @@ process { ...@@ -7,70 +7,76 @@ process {
queue = 'super' queue = 'super'
clusterOptions = '--hold' clusterOptions = '--hold'
withName: trackStart { withName:trackStart {
executor = 'local' executor = 'local'
} }
withName: getBag { withName:getBag {
executor = 'local' executor = 'local'
} }
withName: getData { withName:getData {
queue = 'super' queue = 'super'
} }
withName: parseMetadata { withName:parseMetadata {
executor = 'local' executor = 'local'
} }
withName: trimData { withName:trimData {
queue = 'super' queue = 'super'
} }
withName: getRefInfer { withName:getRefInfer {
queue = 'super' queue = 'super'
} }
withName: downsampleData { withName:downsampleData {
executor = 'local' executor = 'local'
} }
withName: alignSampleData { withName:alignSampleData {
queue = 'super' queue = 'super'
} }
withName: inferMetadata { withName:inferMetadata {
queue = 'super' queue = 'super'
} }
withName: getRef { withName:checkMetadata {
executor = 'local'
}
withName:getRef {
queue = 'super' queue = 'super'
} }
withName: alignData { withName:alignData {
queue = '256GB,256GBv1' queue = '256GB,256GBv1'
} }
withName: dedupData { withName:dedupData {
queue = 'super' queue = 'super'
} }
withName: countData { withName:countData {
queue = 'super' queue = 'super'
} }
withName: makeBigWig { withName:makeBigWig {
queue = 'super' queue = 'super'
} }
withName: fastqc { withName:fastqc {
queue = 'super' queue = 'super'
} }
withName: dataQC { withName:dataQC {
queue = 'super' queue = 'super'
} }
withName: aggrQC { withName:aggrQC {
executor = 'local'
}
withName:uploadInputBag {
executor = 'local' executor = 'local'
} }
withName: uploadInputBag { withName:uploadExecutionRun {
executor = 'local' executor = 'local'
} }
withName: uploadExecutionRun { withName:uploadQC {
executor = 'local' executor = 'local'
} }
withName: uploadQC { withName:uploadProcessedFile {
executor = 'local' executor = 'local'
} }
withName: uploadProcessedFile { withName:uploadOutputBag {
executor = 'local' executor = 'local'
} }
withName: uploadOutputBag { withName:finalizeExecutionRun {
executor = 'local' executor = 'local'
} }
} }
......
workflow/nextflow.config
+ 21
− 15
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...@@ -25,46 +25,49 @@ process { ...@@ -25,46 +25,49 @@ process {
withName:getData { withName:getData {
container = 'gudmaprbk/deriva1.3:1.0.0' container = 'gudmaprbk/deriva1.3:1.0.0'
} }
withName: parseMetadata { withName:parseMetadata {
container = 'gudmaprbk/python3:1.0.0' container = 'gudmaprbk/python3:1.0.0'
} }
withName: trimData { withName:trimData {
container = 'gudmaprbk/trimgalore0.6.5:1.0.0' container = 'gudmaprbk/trimgalore0.6.5:1.0.0'
} }
withName: getRefInfer { withName:getRefInfer {
container = 'gudmaprbk/deriva1.3:1.0.0' container = 'gudmaprbk/deriva1.3:1.0.0'
} }
withName: downsampleData { withName:downsampleData {
container = 'gudmaprbk/seqtk1.3:1.0.0' container = 'gudmaprbk/seqtk1.3:1.0.0'
} }
withName: alignSampleData { withName:alignSampleData {
container = 'gudmaprbk/hisat2.2.1:1.0.0' container = 'gudmaprbk/hisat2.2.1:1.0.0'
} }
withName: inferMetadata { withName:inferMetadata {
container = 'gudmaprbk/rseqc4.0.0:1.0.0' 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' container = 'gudmaprbk/deriva1.3:1.0.0'
} }
withName: alignData { withName:alignData {
container = 'gudmaprbk/hisat2.2.1:1.0.0' container = 'gudmaprbk/hisat2.2.1:1.0.0'
} }
withName: dedupData { withName:dedupData {
container = 'gudmaprbk/picard2.23.9:1.0.0' container = 'gudmaprbk/picard2.23.9:1.0.0'
} }
withName: countData { withName:countData {
container = 'gudmaprbk/subread2.0.1:1.0.0' container = 'gudmaprbk/subread2.0.1:1.0.0'
} }
withName: makeBigWig { withName:makeBigWig {
container = 'gudmaprbk/deeptools3.5.0:1.0.0' container = 'gudmaprbk/deeptools3.5.0:1.0.0'
} }
withName: fastqc { withName:fastqc {
container = 'gudmaprbk/fastqc0.11.9:1.0.0' container = 'gudmaprbk/fastqc0.11.9:1.0.0'
} }
withName: dataQC { withName:dataQC {
container = 'gudmaprbk/rseqc4.0.0:1.0.0' container = 'gudmaprbk/rseqc4.0.0:1.0.0'
} }
withName: aggrQC { withName:aggrQC {
container = 'gudmaprbk/multiqc1.9:1.0.0' container = 'gudmaprbk/multiqc1.9:1.0.0'
} }
withName:uploadInputBag { withName:uploadInputBag {
...@@ -82,6 +85,9 @@ process { ...@@ -82,6 +85,9 @@ process {
withName:uploadOutputBag { withName:uploadOutputBag {
container = 'gudmaprbk/deriva1.3:1.0.0' container = 'gudmaprbk/deriva1.3:1.0.0'
} }
withName:finalizeExecutionRun {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
} }
trace { trace {
...@@ -110,6 +116,6 @@ manifest { ...@@ -110,6 +116,6 @@ manifest {
homePage = 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq' 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.' 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' mainScript = 'rna-seq.nf'
version = 'v0.0.4_indev' version = 'v0.1.0'
nextflowVersion = '>=19.09.0' nextflowVersion = '>=19.09.0'
} }
workflow/rna-seq.nf
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