commit 31052e7c261daff08b124a0a24f40900a830c261
Author: Chloe Quignot <>
Date:   Fri Jun 7 14:29:33 2024 +0200

    add Emilie's changes from other repo: change report from bowtie2 to samtoolsSort

diff --git a/demo_advanced/codes/Snakefile b/demo_advanced/codes/Snakefile
index 325fb5d..e473a91 100644
--- a/demo_advanced/codes/Snakefile
+++ b/demo_advanced/codes/Snakefile
@@ -94,12 +94,7 @@ rule bowtie2:
         fq="data/{sample}.fastq.gz",
         idxFile=rules.bowtieIndex.output,
     output:
-        bam=report(
-            pipe("result/bowtie/{sample}.sam"),
-            caption="report/bowtie2.rst",
-            category="Step 2 Bowtie2",
-        ),
-        # not a good idea because bam files are heavy
+        bam=pipe("result/bowtie/{sample}.sam"),
     log:
         bwtout="result/logs/bowtie/{sample}_align.txt",
         stderr="result/logs/bowtie/{sample}_align.stderr",
@@ -120,7 +115,7 @@ rule bowtie2:
     shell:
         """
           bowtie2 -x {params.idx} -U {input.fq} -p {threads} {params.extra} \
-                  2> {log.bwtout} > {output} 
+                  2> {log.bwtout} > {output}
         """
 
 
@@ -128,7 +123,12 @@ rule samtoolsSort:
     input:
         "result/bowtie/{sample}.sam",
     output:
-        protected("result/bowtie/{sample}.bam"),
+        report(
+            protected("result/bowtie/{sample}.bam"),
+            caption="report/bowtie2.rst",
+            category="Step 2 Bowtie2",
+        ),
+    # not a good idea because bam files are heavy
     log:
         "result/logs/samtools/{sample}.txt",
     benchmark:
diff --git a/demo_advanced/runRnaseq.sh b/demo_advanced/runRnaseq.sh
index 65d5837..0b9b631 100644
--- a/demo_advanced/runRnaseq.sh
+++ b/demo_advanced/runRnaseq.sh
@@ -4,6 +4,9 @@ module load snakemake/snakemake-8.4.6
 
 cd /path/to/the/project/
 
-snakemake --executor cluster-generic --cluster-generic-submit-cmd "qsub -V -l walltime={resources.time_min} -l select=1:ncpus={threads}:mem={resources.mem}" --snakefile codes/Snakefile --profile codes/profile --configfile configfile.yaml &> smkpipeline.txt
+# create directory for the pbs logs
+mkdir pbs
 
-snakemake --executor cluster-generic --cluster-generic-submit-cmd "qsub -V -l walltime={resources.time_min} -l select=1:ncpus={threads}:mem={resources.mem}" --snakefile codes/Snakefile --profile codes/profile --configfile configfile.yaml --report smkRnaseq_report.html 
+snakemake --executor cluster-generic --cluster-generic-submit-cmd "qsub -V -l walltime={resources.time_min} -l select=1:ncpus={threads}:mem={resources.mem} -e pbs/{name}_$PBS_JOBID.err -o pbs/{name}_$PBS_JOBID.out" --snakefile codes/Snakefile --profile codes/profile --configfile configfile.yaml &> smkpipeline.txt
+
+snakemake --executor cluster-generic --cluster-generic-submit-cmd "qsub -V -l walltime={resources.time_min} -l select=1:ncpus={threads}:mem={resources.mem}" --snakefile codes/Snakefile --profile codes/profile --configfile configfile.yaml --report smkRnaseq_report.html