Commit 61515526 authored by Gervaise Henry's avatar Gervaise Henry 🤠

Change some formatting to match cellranger_count

parent c4f7f5d3
Pipeline #4201 passed with stages
in 2 minutes
......@@ -25,7 +25,7 @@ process {
}
withLabel:multiqc {
module = ['multiqc/1.7']
executor = 'super'
executor = 'local'
}
}
......
# Custom Logo
custom_logo: 'bicf_logo.png'
custom_logo_url: 'https://www.utsouthwestern.edu/labs/bioinformatics/'
custom_logo_title: 'Bioinformatics Core Facility'
report_header_info:
- Contact E-mail: 'bicf@utsouthwestern.edu'
- Application Type: 'cellranger_mkfastq'
- Department: 'Bioinformatic Core Facility, Department of Bioinformatics'
# Title to use for the report.
title: BICF CellRanger MKfastq Analysis Report
report_comment: >
This report has been generated by the <a href="https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq"
target="_blank">BICF/cellranger_mkfastq</a> pipeline.
module_order:
- bcl2fastq
- fastqc:
......@@ -21,7 +39,7 @@ module_order:
- custom_content
report_section_order:
Software_Versions:
software_versions:
order: -1100
Software_References:
software_references:
order: -1200
......@@ -8,6 +8,7 @@ params.name = "run"
params.bcl = "$baseDir/../test_data/*.tar.gz"
params.designFile = "$baseDir/../test_data/design.csv"
params.outDir = "$baseDir/output"
params.multiqcConf = "$baseDir/conf/multiqc_config.yaml"
params.references = "$baseDir/../docs/references.md"
// Define List of Files
......@@ -19,6 +20,7 @@ designLocation = Channel
.fromPath(params.designFile)
.ifEmpty { exit 1, "design file not found: ${params.designFile}" }
outDir = params.outDir
multiqcConf = params.multiqcConf
references = params.references
process checkDesignFile {
......@@ -27,15 +29,12 @@ process checkDesignFile {
module 'python/3.6.1-2-anaconda'
input:
file designLocation
output:
file("design.checked.csv") into designPaths
script:
"""
hostname
ulimit -a
......@@ -50,15 +49,12 @@ process untarBCL {
module 'pigz/2.4'
input:
file tar from tarList
output:
file("*") into bclPaths mode flatten
script:
"""
hostname
ulimit -a
......@@ -73,18 +69,15 @@ process mkfastq {
module 'cellranger/3.0.2:bcl2fastq/2.19.1'
input:
each bcl from bclPaths.collect()
file design from designPaths
output:
file("**/outs/**/*.fastq.gz") into fastqPaths
file("**/outs/fastq_path/Stats/Stats.json") into bqcPaths
val "${bcl.baseName}" into bclName
script:
"""
hostname
ulimit -a
......@@ -103,11 +96,9 @@ process fastqc {
val bclName
output:
file("*fastqc.zip") into fqcPaths
script:
"""
hostname
ulimit -a
......@@ -126,11 +117,9 @@ process versions {
input:
output:
file("*.yaml") into yamlPaths
script:
"""
hostname
ulimit -a
......@@ -149,20 +138,17 @@ process multiqc {
module 'multiqc/1.7'
input:
file bqc name "bqc/?/*" from bqcPaths.collect()
file fqc name "fqc/*" from fqcPaths.collect()
file yamlPaths
output:
file("*") into mqcPaths
script:
"""
hostname
ulimit -a
multiqc . -c "$baseDir/conf/multiqc_config.yaml"
multiqc -c $multiqcConf .
"""
}
}
\ No newline at end of file
......@@ -54,7 +54,7 @@ def main():
# Header for HTML
print('''
id: 'Software References'
id: 'software_references'
section_name: 'Software References'
description: 'This section describes references for the tools used.'
plot_type: 'html'
......
File mode changed from 100644 to 100755
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