Skip to content
Snippets Groups Projects
Commit eb035918 authored by mariabernard's avatar mariabernard
Browse files

Snakemake 1000RNASeq chicken/calling : update SLURM.sh

parent 78490710
No related branches found
No related tags found
No related merge requests found
......@@ -28,6 +28,7 @@ snakemake -s $WORKFLOW_DIR/Snakefile_calling --printshellcmds --jobs 200 \
--configfile config_calling.yaml.example \
--cluster-config $WORKFLOW_DIR/resources_SLURM.yaml \
--cluster "sbatch -p {cluster.partition} --cpus-per-task={cluster.cpu} --mem-per-cpu={cluster.mem} --error=logs/%x.stderr --output=logs/%x.stdout " --latency-wait 30 \
Results/Summary/Log_TrimGalore_summary.tsv Results/Summary/Log_STAR_Aln_1_summary.tsv Results/Summary/Log_STAR_Aln_2_summary.tsv \
Results/Summary/RSEM_multimap_summary_${PREFIX}_genes_expected_count.tsv \
Results/Summary/RSEM_uniqmap_summary_${PREFIX}_genes_expected_count.tsv \
Results/Summary/RSEM_multimap_summary_${PREFIX}_genes_FPKM.tsv \
......@@ -41,11 +42,12 @@ snakemake -s $WORKFLOW_DIR/Snakefile_calling --printshellcmds --jobs 200 \
Results/Summary/RSEM_multimap_summary_${PREFIX}_isoforms_TPM.tsv \
Results/Summary/RSEM_uniqmap_summary_${PREFIX}_isoforms_TPM.tsv
# For RSEM quantification only
# For GATK calling only
PREFIX=?? # your sample_config TSV file whithout extension
snakemake -s $WORKFLOW_DIR/Snakefile_calling --printshellcmds --jobs 200 \
--configfile config_calling.yaml.example \
--cluster-config $WORKFLOW_DIR/resources_SLURM.yaml \
--cluster "sbatch -p {cluster.partition} --cpus-per-task={cluster.cpu} --mem-per-cpu={cluster.mem} --error=logs/%x.stderr --output=logs/%x.stdout " --latency-wait 30 \
Results/Summary/Log_TrimGalore_summary.tsv Results/Summary/Log_STAR_Aln_1_summary.tsv Results/Summary/Log_STAR_Aln_2_summary.tsv \
Results/GATK/${PREFIX}_SNP.vcf.gz\
Results/GATK/${PREFIX}_INDEL.vcf.gz
\ No newline at end of file
Results/GATK/${PREFIX}_INDEL.vcf.gz
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment