Snakemake 1000RNASeq chicken/calling : update SLURM.sh

Snakemake/1000RNASeq_chicken/calling/SLURM.sh

@@ -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