Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
Dear DSchreyer
i have the input file like this
sample,fastq_1,fastq_2
270502,/path/270502_S0_L001/270502_S0_L001_R1_001.fastq.gz,/path/270502_S0_L001_R2_001.fastq.gz
when i ran this, the circdna nfcore pipleine print out only this,
Cannot invoke "org.eclipse.jgit.lib.ObjectId.name()" because the return value of "org.eclipse.jgit.lib.Ref.getObjectId()" is null
Dear DSchreyer i have the input file like this sample,fastq_1,fastq_2 270502,/path/270502_S0_L001/270502_S0_L001_R1_001.fastq.gz,/path/270502_S0_L001_R2_001.fastq.gz
and my run.sh script look like this
! /bin/bash
module load nextflow export NXF_SINGULARITY_CACHEDIR=/data/SCLC-AUTOPSY/nextflow/nxf_singularity_cache; export SINGULARITY_CACHEDIR=/data/SCLC-AUTOPSY/nextflow/nxf_singularity_cache/.singularity; export TMPDIR=/lscratch/$SLURM_JOB_ID export NXF_JVM_ARGS="-Xms2g -Xmx4g"
sbatch <<EOT
!/bin/bash
SBATCH --job-name=nextflow-main
SBATCH --cpus-per-task=4
SBATCH --mem=40G
SBATCH --gres=lscratch:200
SBATCH --time=36:00:00
nextflow run nf-core/circdna \ -profile biowulf \ --input /path/matched_samplesheet.csv \ --outdir path/results_batch \ --genome GRCh37 \ --igenomes_base /path/igenomes_nf \ -resume
exit 0 EOT
when i ran this, the circdna nfcore pipleine print out only this, Cannot invoke "org.eclipse.jgit.lib.ObjectId.name()" because the return value of "org.eclipse.jgit.lib.Ref.getObjectId()" is null