example PBS slurm

src/slurm.pbs

-#!/bin/sh
-
-#SBATCH --job-name=nextflow
-#SBATCH --time=1-00:00:00             # Délai max = 7 jours
-#SBATCH --cpus-per-task=1
-#SBATCH --mem=4G
-#SBATCH --ntasks=1
-#SBATCH --output=/sps/lbmc/camille/results/Cous1_results/nextflow_%j.log
-#SBATCH --licenses=sps
-
-#####################################
-SCRATCH=/sps/lbmc/camille/mars_seq/src
-
-/sps/lbmc/camille/nextflow/src/nextflow run /sps/lbmc/camille/mars_seq/src/Mars_seq.nf -c /sps/lbmc/camille/mars_seq/src/Mars_seq.config -profile ccin2p3 \
---fastq "/sps/lbmc/camille/Sequences/cousines/Cous1_R{1,2}.fastq.gz" \
---tags "/sps/lbmc/camille/Sequences/tags/tags_17_26.fa" \
---reference "/sps/lbmc/camille/Sequences/Genome/Gallus_gallus_ERRC_noPolyA.fa" \
---gtf "/sps/lbmc/camille/Sequences/Genome/test.gtf" \
---index "/sps/lbmc/camille/Sequences/Genome/Gallus_no_polyA/" \
---results "/sps/lbmc/camille/results/Cous1_results/" \
---whitelist "/sps/lbmc/camille/Sequences/expected_whitelist.txt" \
---gene_map "/sps/lbmc/camille/Sequences/tx2gene/newtx2geneGallusgallu_MT_ERCCincluded" \
--ansi-log \
--w "/sps/lbmc/camille/work" 

src/slurm_exemple.pbs

+#!/bin/sh
+
+#SBATCH --job-name=nextflow
+#SBATCH --ntasks=1
+#SBATCH --output=/sps/lbmc/evallin/results/EV164/nextflow_%j.log
+#SBATCH --licenses=sps
+#SBATCH --time=1-00:00:00             # Délai max = 7 jours
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=4G
+
+#####################################
+
+/sps/lbmc/evallin/mars_seq/src/Elodie/nextflow run /sps/lbmc/evallin/mars_seq/src/Mars_seq.nf -c /sps/lbmc/evallin/mars_seq/src/Mars_seq.config -profile ccin2p3 \
+--fastq "/sps/lbmc/evallin/Sequences/EV164_R{1,2}.fastq.gz" \
+--tags "/sps/lbmc/evallin/Sequences/tags/tags_1_7_2_6.fa" \
+--reference "/sps/lbmc/evallin/Sequences/Genome_Hom/Homo_sapiens_ERCC_noPolyA.fa" \
+--gtf "/sps/lbmc/evallin/Sequences/Genome_Hom/Homo_sapiens_ercc.gtf" \
+--index "/sps/lbmc/evallin/Sequences/Genome_Hom/Index_Homo_sapiens_noPolyA/" \
+--results "/sps/lbmc/evallin/results/EV164/" \
+--whitelist "/sps/lbmc/evallin/Sequences/expected_whitelist.txt" \
+--gene_map "/sps/lbmc/evallin/Sequences/tx2gene/2023_01_24_new_Homo_sapiens_tx2gene_sansUnderscore" \
+-ansi-log \
+-resume \
+-w "/sps/lbmc/evallin/work" 
+