relocated template taxprofiler

Daniel-VM · Aug 30, 2024 · 19472f4 · 19472f4
1 parent 043383c
commit 19472f4
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Showing 6 changed files with 11 additions and 11 deletions.
diff --git a/bu_isciii/templates/characterization/RESULTS/lablog_taxprofiling_results b/bu_isciii/templates/characterization/RESULTS/lablog_taxprofiling_results
diff --git a/...n/ANALYSIS/ANALYSIS02_TAXPROFILING/lablog → ...ag/ANALYSIS/ANALYSIS01_TAXPROFILER/lablog b/...n/ANALYSIS/ANALYSIS02_TAXPROFILING/lablog → ...ag/ANALYSIS/ANALYSIS01_TAXPROFILER/lablog
@@ -65,11 +65,11 @@ cat <<EOF > taxprofiler.sbatch
 #SBATCH --chdir $scratch_dir
 
 # module load Nextflow/23.10.0 singularity
-export NXF_OPTS="-Xms500M -Xmx10G"
+export NXF_OPTS="-Xms500M -Xmx6G"
 
 nextflow run /data/bi/pipelines/nf-core-taxprofiler/nf-core-taxprofiler-1.1.8 \\
     -profile singularity \\
-    -c ../../DOC/hpc_slurm_taxprofiler.config \\
+    -c ../../DOC/taxprofiler.config \\
     --input samplesheet.csv \\
     --outdir ./ \\
     --databases ../../DOC/databasesheet.csv \\

diff --git a/...acterization/ANALYSIS/lablog_taxprofiling → ...templates/mag/ANALYSIS/lablog_taxprofiler b/...acterization/ANALYSIS/lablog_taxprofiling → ...templates/mag/ANALYSIS/lablog_taxprofiler
@@ -3,4 +3,4 @@ mkdir -p 00-reads
 cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R1*.fastq.gz %_R1.fastq.gz" | bash; cd -
 cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R2*.fastq.gz %_R2.fastq.gz" | bash; cd -
 
-mv ANALYSIS02_TAXPROFILING $(date '+%Y%m%d')_ANALYSIS02_TAXPROFILING
+mv ANALYSIS01_TAXPROFILER $(date '+%Y%m%d')_ANALYSIS01_TAXPROFILER
diff --git a/...es/characterization/DOC/databasesheet.csv → ...sciii/templates/mag/DOC/databasesheet.csv b/...es/characterization/DOC/databasesheet.csv → ...sciii/templates/mag/DOC/databasesheet.csv
diff --git a/...rization/DOC/hpc_slurm_taxprofiler.config → ...ciii/templates/mag/DOC/taxprofiler.config b/...rization/DOC/hpc_slurm_taxprofiler.config → ...ciii/templates/mag/DOC/taxprofiler.config
diff --git a/bu_isciii/templates/mag/RESULTS/lablog_taxprofiler_results b/bu_isciii/templates/mag/RESULTS/lablog_taxprofiler_results
@@ -0,0 +1,8 @@
+DELIVERY_FOLDER="$(date '+%Y%m%d')_entrega01"
+mkdir -p $DELIVERY_FOLDER/taxprofiler
+
+# Taxprofiling service
+cd $DELIVERY_FOLDER/taxprofiler
+
+# Links to reports
+ln -s ../../../ANALYSIS/*ANALYSIS01_TAXPROFILER/results/multiqc/multiqc_report.html .