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Commit 5780ec66 authored by Jules Sabban's avatar Jules Sabban
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Make params file usable in command line

parent 031fce27
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......@@ -19,7 +19,27 @@ An example of the params.config and fastqScreen are available in the assets fold
Example of a basic command line the launch the pipeline is (from the nextflow folder) :
```bash
sbatch -J nf-illumina_BHNKY7DRX2_1 -p wflowq -t 3-00 --mem 5GB --wrap="module load bioinfo/Nextflow-v21.04.1; cd /home/sbsuser/work/data/NovaSeq/230116_A00318_0372_BHNKY7DRX2_Lane1_1673933427_10x/nextflow; nextflow run /work/sbsuser/test/jules/VisualStudioSources/wf-illumina-nf/main.nf -profile prod -ansi-log false"
sbatch -J nf-illumina_BHNKY7DRX2_1 -p wflowq -t 3-00 --mem 5GB --wrap="module load bioinfo/Nextflow-v21.04.1; cd /home/sbsuser/work/data/NovaSeq/230116_A00318_0372_BHNKY7DRX2_Lane1_1673933427_10x/nextflow; nextflow run /work/sbsuser/test/jules/VisualStudioSources/wf-illumina-nf/main.nf -profile prod -ansi-log false -params-file ../params.yml"
```
Tha YAML parameter file must looks like :
```
inputdir: "/home/sbsuser/work/Nextflow/wf-illumina-nf/data_test/NovaSeq/211129_A00318_0259_AHNMTTDSX2_Lane1_1638345606_dna"
project: 'GwOAK_small'
isMultiplex: true
dataNature: "DNA"
pairedEnd: true
splitReads: true # // ????
referenceGenome: "/save/ng6/TODO/HiSeqIndexedGenomes/new_struct/Quercus_robur/genome/GCA_900291515.1/BWA/GCA_900291515.1_Q_robur_v1_genomic.fna"
addBankForConta: ""
runName: "ContaComparison"
sequencer: "NovaSeq"
run_date: "2022"
machineID: "NOVA"
fcID: "HNMTTDSX2"
lane: "1"
demuxUniqueness: "1638345606"
```
NB : for the moment, the case of multi-projects lane is not managed !
\ No newline at end of file
----------------------------------------------------
GeT/template v${version}
----------------------------------------------------
Run Name: $runName
<% if (success){
out << "## GeT/template execution completed successfully! ##"
} else {
out << """####################################################
## GeT/template execution completed unsuccessfully! ##
####################################################
The exit status of the task that caused the workflow execution to fail was: $exitStatus.
The full error message was:
${errorReport}
"""
} %>
The workflow was completed at $dateComplete (duration: $duration)
The command used to launch the workflow was as follows:
$commandLine
Pipeline Configuration:
-----------------------
<% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
--
GeT/template
https://forgemia.inra.fr/get-nextflow-ngl-bi/template-nf
inputdir="/home/sbsuser/work/data/NovaSeq/230116_A00318_0372_BHNKY7DRX2_Lane1_1673933427_10x"
project = "MAGICs"
isMultiplex = true
dataNature = "DNA"
splitReads = true
referenceGenome = ""
addBankForConta = ""
runName="Test_10X"
sequencer="NovaSeq"
run_date="230116"
machineID="NOVA"
fcID="BHNKY7DRX2"
lane="1"
demuxUniqueness="1673933427"
......@@ -10,13 +10,14 @@ params {
outdir = "./" // base output directory for all analysis
}
import java.text.SimpleDateFormat
SimpleDateFormat uniqueness_format = new SimpleDateFormat("yyyMMddHHmmss")
params.samplesheet = params.inputdir.toString() + "/SampleSheet.csv"
params.data = params.inputdir.toString() + "/" + params.project.toString()
System.out.println "Lecture du fichier de configuration du run : $launchDir/../params.config"
includeConfig "$launchDir/../params.config"
System.out.println "Lecture du fichier de configuration du run : PARAMS"
// Dynamic params
import java.text.SimpleDateFormat
SimpleDateFormat uniqueness_format = new SimpleDateFormat("yyyyMMddHHmmss")
params {
nf_uniqueness = uniqueness_format.format(new Date())
outdir= params.inputdir + "/nextflow/" + nf_uniqueness
......
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