Bonjour,
Je veux lancer NF-core avec les modules ci-dessous, mais j'ai une erreur concernant jGit, l'outil de Java avec Git.
Pourriez-vous m'éclairer sur ce qu'il manque ?
Voici mon code (testé avec les deux versions nextflow ,nf-core mentionnés ) :
module load singularity
module load openjdk/22.0.1
module load java-jdk/11.0.9.1
module load nextflow/24.04.1 #& 24.10.4
module load nf-core/2.7.2 #& 3.2.0
export JAVA_LD_LIBRARY_PATH=/shared/ifbstor1/software/miniconda/envs/nextflow-24.04.1/lib/jvm/lib/server/
export JAVA_HOME=/shared/ifbstor1/software/miniconda/envs/nextflow-24.04.1
samplesheet="samplesheet_patient_M.csv" # csv with : sample_name,fastq_1,fastq_2,strandedness{auto/forward/reverse}
###
### For HUMAN :
###
hs_fasta_ref="/shared/bank/homo_sapiens/GRCh38.p14/Ensembl_110/fasta/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
hs_gtf_ref="/shared/bank/homo_sapiens/GRCh38.p14/Ensembl_110/gtf/Homo_sapiens.GRCh38.110.gtf" #> with "chr" in 1st col
/shared/ifbstor1/software/miniconda/envs/nextflow-24.04.1/bin/nextflow run nf-core/rnaseq -profile ifb_core \
--input ${samplesheet} \
--fasta ${hs_fasta_ref} \
--gtf ${hs_gtf_ref} \
--aligner 'star_salmon' \
--outdir ${out_dir}
L erreur:
DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /shared/home/mkondili/.nextflow/scm
DEBUG nextflow.scm.AssetManager - Project manifest does not exist: /shared/home/mkondili/.nextflow/assets/nf-core/rnaseq/nextflow.config (No such file or directory)
DEBUG nextflow.scm.AssetManager - Git config: /shared/home/mkondili/.nextflow/assets/nf-core/rnaseq/.git/config; branch: null; remote: origin; url: https://github.com/nf-core/rnaseq.git
DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
DEBUG nextflow.scm.AssetManager - Git config: /shared/home/mkondili/.nextflow/assets/nf-core/rnaseq/.git/config; branch: null; remote: origin; url: https://github.com/nf-core/rnaseq.git
INFO nextflow.cli.CmdRun - Pulling nf-core/rnaseq ...
DEBUG nextflow.scm.AssetManager - Pull pipeline nf-core/rnaseq -- Using local path: /shared/home/mkondili/.nextflow/assets/nf-core/rnaseq
ERROR nextflow.cli.Launcher - @unknown
java.lang.NullPointerException: Cannot invoke "org.eclipse.jgit.lib.ObjectId.name()" because the return value of "org.eclipse.jgit.lib.Ref.getObjectId()" is null
at nextflow.scm.AssetManager.getCurrentRevisionAndName(AssetManager.groovy:742)
at nextflow.scm.AssetManager.download(AssetManager.groovy:663)
at nextflow.cli.CmdRun.getScriptFile0(CmdRun.groovy:599)
at nextflow.cli.CmdRun.getScriptFile(CmdRun.groovy:532)
at nextflow.cli.CmdRun.run(CmdRun.groovy:325)
at nextflow.cli.Launcher.run(Launcher.groovy:503)
at nextflow.cli.Launcher.main(Launcher.groovy:658)
Si besoin de plus d informations pour mieux comprendre l'erreur, je pourrai les fournir.
bonne journée