Commit 83373355 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Add dev tracking param, version 2.1.2

parent 6b7f1c7f
Pipeline #7359 failed with stages
in 13 seconds
# v2.1.1 # v2.1.2
**UserFacing** **UserFacing**
* Check Design File for spaces in name and file contents * Check Design File for spaces in name and file contents
* Update design example, README, and astrocyte.yml with current barcode IDs * Update design example, README, and astrocyte.yml with current barcode IDs
...@@ -20,7 +20,7 @@ ...@@ -20,7 +20,7 @@
* note: pipeline checks for spaces and exits prematurely if found * note: pipeline checks for spaces and exits prematurely if found
* If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable * If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable
* note: if multiple bcl files are detected then cellranger_count design file is not created * note: if multiple bcl files are detected then cellranger_count design file is not created
* If too many (or too large) .tar(.gz) bcl files are placed in one run, aws runs appears to fail possibly due to timeount on staging * If too many (or too large) .tar(.gz) bcl files are placed in one run, aws runs appears to fail possibly due to timeout on staging
# v1.3.1 # v1.3.1
**User Facing** **User Facing**
......
...@@ -32,7 +32,7 @@ bclCount = Channel ...@@ -32,7 +32,7 @@ bclCount = Channel
.count() .count()
// Define regular variables // Define regular variables
pipelineVersion = "2.1.1" pipelineVersion = "2.1.2"
name = params.name name = params.name
designLocation = Channel designLocation = Channel
.fromPath(params.designFile) .fromPath(params.designFile)
...@@ -62,6 +62,7 @@ references = Channel.fromPath("${baseDir}/../docs/references.md") ...@@ -62,6 +62,7 @@ references = Channel.fromPath("${baseDir}/../docs/references.md")
* trackStart: track start of pipeline * trackStart: track start of pipeline
*/ */
params.ci = false params.ci = false
params.dev = false
process trackStart { process trackStart {
script: script:
""" """
...@@ -77,7 +78,8 @@ process trackStart { ...@@ -77,7 +78,8 @@ process trackStart {
"astrocyte": ${params.astrocyte}, \ "astrocyte": ${params.astrocyte}, \
"status": "started", \ "status": "started", \
"nextflowVersion": "${workflow.nextflow.version}", "nextflowVersion": "${workflow.nextflow.version}",
"ci": ${params.ci}}' \ "ci": ${params.ci},
"dev": ${param.dev}}' \
"https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking" "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
""" """
} }
......
...@@ -47,6 +47,6 @@ manifest { ...@@ -47,6 +47,6 @@ manifest {
homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq' homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcls and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.' description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcls and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
mainScript = 'main.nf' mainScript = 'main.nf'
version = '2.1.1' version = '2.1.2'
nextflowVersion = '>=0.31.0' nextflowVersion = '>=0.31.0'
} }
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