Differenze

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--- calcoloscientifico:userguide:nextflow [05/11/2023 19:07] – creata fabio.spataro
+++ calcoloscientifico:userguide:nextflow [04/08/2026 16:05] (versione attuale) – fabio.spataro
@@ Linea 2: / Linea 2: @@
 [[https://www.nextflow.io/|Nextflow]]
+Available versions of Nextflow:
+^ Nextflow  ^
+| 23.10.0   |
+| 24.04.4   |
+| 25.04.2   |
+| 26.04.6   |
 === Job Nextflow ===
@@ Linea 10: / Linea 19: @@
 #!/bin/bash --login
 #SBATCH --job-name=nextflow_chipseq
-#SBATCH --output=%x.o%j
+#SBATCH --output=%x.%j.out
-#SBATCH --error=%x.e%j
+#SBATCH --error=%x.%j.err
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=1
@@ Linea 23: / Linea 32: @@
 shopt -q login_shell || exit 1
-module load nextflow/23.10.0
+module load nextflow/26.04.6
 # chipseq
@@ Linea 29: / Linea 38: @@
     -r 2.0.0 \
     -profile test,singularity \
-    -with-singularity "$CONTAINER" \
+    -with-singularity "$NXF_CONTAINER" \
     --outdir "${SLURM_JOB_NAME}.${SLURM_JOB_ID}"
+</code>
+In the event of errors occurring only with version 26.04.6 and the ''nf-core/sarek'' pipeline, it may be necessary to define the following environment variable:
+<code>
+export NXF_SYNTAX_PARSER="v1"
 </code>