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Commit 554ef719 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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De-containerize (remove cellranger 2.1.1 because no BioHPC module)

parent 5677b2e2
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2 merge requests!73Develop,!71De containerize
...@@ -2,8 +2,8 @@ before_script: ...@@ -2,8 +2,8 @@ before_script:
- module load astrocyte - module load astrocyte
- module load python/3.6.1-2-anaconda - module load python/3.6.1-2-anaconda
- pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1 - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
- module load singularity/3.0.2
- module load nextflow/20.01.0 - module load nextflow/20.01.0
- module load singularity/3.0.2
- mkdir -p test_data/hu.v2s1r500 - mkdir -p test_data/hu.v2s1r500
- mkdir -p test_data/hu.v3s1r500 - mkdir -p test_data/hu.v3s1r500
- mkdir -p test_data/mu.v3s1r500 - mkdir -p test_data/mu.v3s1r500
...@@ -44,29 +44,8 @@ astrocyte_cli: ...@@ -44,29 +44,8 @@ astrocyte_cli:
- master - master
- tags - tags
script: script:
- singularity run 'docker://bicf/cellranger2.1.1:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2 - module load cellranger/2.1.1
artifacts: - cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
name: "$CI_JOB_NAME"
when: always
paths:
- test/outs/web_summary.html
expire_in: 2 days
retry:
max: 0
when:
- always
2.2.2_test:
stage: container_test
only:
- branches
except:
refs:
- develop
- master
- tags
script:
- singularity run 'docker://bicf/cellranger2.2.0:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
when: always when: always
...@@ -88,7 +67,8 @@ astrocyte_cli: ...@@ -88,7 +67,8 @@ astrocyte_cli:
- master - master
- tags - tags
script: script:
- singularity run 'docker://bicf/cellranger3.0.2:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2 - module load cellranger/3.0.2
- cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
when: always when: always
...@@ -110,7 +90,8 @@ astrocyte_cli: ...@@ -110,7 +90,8 @@ astrocyte_cli:
- master - master
- tags - tags
script: script:
- singularity run 'docker://bicf/cellranger3.1.0:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2 - module load cellranger/3.1.0
- cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
when: always when: always
......
...@@ -150,7 +150,6 @@ workflow_parameters: ...@@ -150,7 +150,6 @@ workflow_parameters:
choices: choices:
- ['3.1.0', '3.1.0'] - ['3.1.0', '3.1.0']
- ['3.0.2', '3.0.2'] - ['3.0.2', '3.0.2']
- ['2.2.0', '2.2.0']
- ['2.1.1', '2.1.1'] - ['2.1.1', '2.1.1']
required: true required: true
description: | description: |
......
...@@ -20,10 +20,6 @@ process { ...@@ -20,10 +20,6 @@ process {
cpus = 2 cpus = 2
memory = '30 GB' memory = '30 GB'
} }
withLabel: count220 {
cpus = 2
memory = '30 GB'
}
withLabel: count302 { withLabel: count302 {
cpus = 2 cpus = 2
memory = '30 GB' memory = '30 GB'
......
...@@ -52,11 +52,6 @@ params { ...@@ -52,11 +52,6 @@ params {
} }
} }
singularity {
enabled = true
cacheDir = '/project/BICF/BICF_Core/shared/gudmap/singularity_cache/'
}
env { env {
http_proxy = 'http://proxy.swmed.edu:3128' http_proxy = 'http://proxy.swmed.edu:3128'
https_proxy = 'http://proxy.swmed.edu:3128' https_proxy = 'http://proxy.swmed.edu:3128'
......
...@@ -12,9 +12,6 @@ process { ...@@ -12,9 +12,6 @@ process {
withLabel: count211 { withLabel: count211 {
queue = '128GB,256GB,256GBv1,384GB' queue = '128GB,256GB,256GBv1,384GB'
} }
withLabel: count220 {
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: count302 { withLabel: count302 {
queue = '128GB,256GB,256GBv1,384GB' queue = '128GB,256GB,256GBv1,384GB'
} }
......
...@@ -35,10 +35,6 @@ if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') { ...@@ -35,10 +35,6 @@ if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') {
print("Cellranger Version 2.1.1 requires kitVersion 2") print("Cellranger Version 2.1.1 requires kitVersion 2")
System.exit(32) System.exit(32)
} }
if (params.kitVersion == "3GEXv3" && params.version == '2.2.0') {
print("Cellranger Version 2.2.0 requires kitVersion 2")
System.exit(32)
}
// Define variables if astrocyte (or from config) // Define variables if astrocyte (or from config)
if (params.astrocyte) { if (params.astrocyte) {
...@@ -118,6 +114,7 @@ process trackStart { ...@@ -118,6 +114,7 @@ process trackStart {
*/ */
process checkDesignFile { process checkDesignFile {
tag "${name}" tag "${name}"
module 'python/3.6.1-2-anaconda'
input: input:
file designLocation file designLocation
...@@ -149,26 +146,21 @@ samples = designPaths ...@@ -149,26 +146,21 @@ samples = designPaths
// Duplicate variables // Duplicate variables
samples.into { samples.into {
samples211 samples211
samples220
samples302 samples302
samples310 samples310
} }
refLocation.into { refLocation.into {
refLocation211 refLocation211
refLocation220
refLocation302 refLocation302
refLocation310 refLocation310
} }
expectCells211 = expectCells expectCells211 = expectCells
expectCells220 = expectCells
expectCells302 = expectCells expectCells302 = expectCells
expectCells310 = expectCells expectCells310 = expectCells
forceCells211 = forceCells forceCells211 = forceCells
forceCells220 = forceCells
forceCells302 = forceCells forceCells302 = forceCells
forceCells310 = forceCells forceCells310 = forceCells
chemistryParam211 = chemistryParam chemistryParam211 = chemistryParam
chemistryParam220 = chemistryParam
chemistryParam302 = chemistryParam chemistryParam302 = chemistryParam
chemistryParam310 = chemistryParam chemistryParam310 = chemistryParam
...@@ -179,6 +171,7 @@ process count211 { ...@@ -179,6 +171,7 @@ process count211 {
tag "${sample}" tag "${sample}"
publishDir "${outDir}/${task.process}", mode: 'copy' publishDir "${outDir}/${task.process}", mode: 'copy'
queue '128GB,256GB,256GBv1,384GB' queue '128GB,256GB,256GBv1,384GB'
module 'cellranger/2.1.1'
input: input:
set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples211 set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples211
...@@ -217,50 +210,6 @@ process count211 { ...@@ -217,50 +210,6 @@ process count211 {
} }
} }
/*
* count220: run cellranger count version 2.2.0
*/
process count220 {
queue '128GB,256GB,256GBv1,384GB'
tag "${sample}"
publishDir "${outDir}/${task.process}", mode: 'copy'
input:
set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples220
file ref from refLocation220.first()
expectCells220
forceCells220
chemistryParam220
output:
file("**/outs/**") into outPaths220
file("*_metrics_summary.tsv") into metricsSummary220
when:
version == '2.2.0'
script:
if (forceCells220 == 0) {
"""
hostname
ulimit -u 16384
ulimit -a
bash ${baseDir}/scripts/filename_check.sh -r ${ref}
cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells220} --chemistry=${chemistryParam220}
sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
"""
}
else {
"""
hostname
ulimit -u 16384
ulimit -a
bash ${baseDir}/scripts/filename_check.sh -r ${ref}
cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells220} --chemistry=${chemistryParam220}
sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
"""
}
}
/* /*
* count302: run cellranger count version 3.0.2 * count302: run cellranger count version 3.0.2
...@@ -269,6 +218,7 @@ process count302 { ...@@ -269,6 +218,7 @@ process count302 {
tag "${sample}" tag "${sample}"
publishDir "${outDir}/${task.process}", mode: 'copy' publishDir "${outDir}/${task.process}", mode: 'copy'
queue '128GB,256GB,256GBv1,384GB' queue '128GB,256GB,256GBv1,384GB'
module 'cellranger/3.0.2'
input: input:
set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz") from samples302 set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz") from samples302
...@@ -314,6 +264,7 @@ process count310 { ...@@ -314,6 +264,7 @@ process count310 {
tag "${sample}" tag "${sample}"
publishDir "${outDir}/${task.process}", mode: 'copy' publishDir "${outDir}/${task.process}", mode: 'copy'
queue '128GB,256GB,256GBv1,384GB' queue '128GB,256GB,256GBv1,384GB'
module 'cellranger/3.1.0'
input: input:
set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz") from samples310 set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz") from samples310
...@@ -379,7 +330,7 @@ process versions { ...@@ -379,7 +330,7 @@ process versions {
} }
// Collect all metrics summaries reguardless of cellranger version // Collect all metrics summaries reguardless of cellranger version
metricsSummary = metricsSummary211.mix(metricsSummary220, metricsSummary302, metricsSummary310) metricsSummary = metricsSummary211.mix(metricsSummary302, metricsSummary310)
/* /*
* multiqc: create multiqc report * multiqc: create multiqc report
......
...@@ -22,30 +22,6 @@ profiles { ...@@ -22,30 +22,6 @@ profiles {
} }
} }
process {
withName:checkDesignFile {
container = 'bicf/python3:2.0.0'
}
withName:count211 {
container = 'bicf/cellranger2.1.1:2.0.0'
}
withName:count220 {
container = 'bicf/cellranger2.2.0:2.0.0'
}
withName:count302 {
container = 'bicf/cellranger3.0.2:2.0.0'
}
withName:count310 {
container = 'bicf/cellranger3.1.0:2.0.0'
}
withName:versions {
container = 'bicf/python3:2.0.0'
}
withName:multiqc {
container = 'bicf/multiqc:2.0.0'
}
}
trace { trace {
enabled = true enabled = true
file = 'pipeline_trace.txt' file = 'pipeline_trace.txt'
......
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