From 19472f4722fda94d25dcb41aebda494e02ad9419 Mon Sep 17 00:00:00 2001
From: Dani VM <da.valle@isciii.es>
Date: Fri, 30 Aug 2024 10:14:32 +0200
Subject: [PATCH] relocated template taxprofiler

---
 .../characterization/RESULTS/lablog_taxprofiling_results  | 8 --------
 .../ANALYSIS/ANALYSIS01_TAXPROFILER}/lablog               | 4 ++--
 .../ANALYSIS/lablog_taxprofiler}                          | 2 +-
 .../{characterization => mag}/DOC/databasesheet.csv       | 0
 .../DOC/taxprofiler.config}                               | 0
 .../templates/mag/RESULTS/lablog_taxprofiler_results      | 8 ++++++++
 6 files changed, 11 insertions(+), 11 deletions(-)
 delete mode 100644 bu_isciii/templates/characterization/RESULTS/lablog_taxprofiling_results
 rename bu_isciii/templates/{characterization/ANALYSIS/ANALYSIS02_TAXPROFILING => mag/ANALYSIS/ANALYSIS01_TAXPROFILER}/lablog (96%)
 rename bu_isciii/templates/{characterization/ANALYSIS/lablog_taxprofiling => mag/ANALYSIS/lablog_taxprofiler} (78%)
 rename bu_isciii/templates/{characterization => mag}/DOC/databasesheet.csv (100%)
 rename bu_isciii/templates/{characterization/DOC/hpc_slurm_taxprofiler.config => mag/DOC/taxprofiler.config} (100%)
 create mode 100755 bu_isciii/templates/mag/RESULTS/lablog_taxprofiler_results

diff --git a/bu_isciii/templates/characterization/RESULTS/lablog_taxprofiling_results b/bu_isciii/templates/characterization/RESULTS/lablog_taxprofiling_results
deleted file mode 100644
index 7d5cce5cf..000000000
--- a/bu_isciii/templates/characterization/RESULTS/lablog_taxprofiling_results
+++ /dev/null
@@ -1,8 +0,0 @@
-DELIVERY_FOLDER="$(date '+%Y%m%d')_entrega01"
-mkdir -p $DELIVERY_FOLDER/taxprofiling
-
-# Taxprofiling service
-cd $DELIVERY_FOLDER/taxprofiling
-
-# Links to reports
-ln -s ../../../ANALYSIS/*ANALYSIS02_TAXPROFILING/results/multiqc/multiqc_report.html .
diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS02_TAXPROFILING/lablog b/bu_isciii/templates/mag/ANALYSIS/ANALYSIS01_TAXPROFILER/lablog
similarity index 96%
rename from bu_isciii/templates/characterization/ANALYSIS/ANALYSIS02_TAXPROFILING/lablog
rename to bu_isciii/templates/mag/ANALYSIS/ANALYSIS01_TAXPROFILER/lablog
index e16eab703..06bd2f6bf 100644
--- a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS02_TAXPROFILING/lablog
+++ b/bu_isciii/templates/mag/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/bu_isciii/templates/characterization/ANALYSIS/lablog_taxprofiling b/bu_isciii/templates/mag/ANALYSIS/lablog_taxprofiler
similarity index 78%
rename from bu_isciii/templates/characterization/ANALYSIS/lablog_taxprofiling
rename to bu_isciii/templates/mag/ANALYSIS/lablog_taxprofiler
index e4a813bf5..f6a3f119b 100644
--- a/bu_isciii/templates/characterization/ANALYSIS/lablog_taxprofiling
+++ b/bu_isciii/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 $(date '+%Y%m%d')_ANALYSIS01_TAXPROFILER
diff --git a/bu_isciii/templates/characterization/DOC/databasesheet.csv b/bu_isciii/templates/mag/DOC/databasesheet.csv
similarity index 100%
rename from bu_isciii/templates/characterization/DOC/databasesheet.csv
rename to bu_isciii/templates/mag/DOC/databasesheet.csv
diff --git a/bu_isciii/templates/characterization/DOC/hpc_slurm_taxprofiler.config b/bu_isciii/templates/mag/DOC/taxprofiler.config
similarity index 100%
rename from bu_isciii/templates/characterization/DOC/hpc_slurm_taxprofiler.config
rename to bu_isciii/templates/mag/DOC/taxprofiler.config
diff --git a/bu_isciii/templates/mag/RESULTS/lablog_taxprofiler_results b/bu_isciii/templates/mag/RESULTS/lablog_taxprofiler_results
new file mode 100755
index 000000000..d6231a54b
--- /dev/null
+++ b/bu_isciii/templates/mag/RESULTS/lablog_taxprofiler_results
@@ -0,0 +1,8 @@
+DELIVERY_FOLDER="$(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 .