created tempalte for mag_all

Daniel-VM · Sep 3, 2024 · e1f4c6e · e1f4c6e
1 parent 0eac72c
commit e1f4c6e
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Showing 5 changed files with 33 additions and 7 deletions.
diff --git a/...es/mag/ANALYSIS/ANALYSIS01_MAG_ALL/lablog → ...es/mag/ANALYSIS/ANALYSIS03_MAG_ALL/lablog b/...es/mag/ANALYSIS/ANALYSIS01_MAG_ALL/lablog → ...es/mag/ANALYSIS/ANALYSIS03_MAG_ALL/lablog
@@ -11,14 +11,14 @@ done >> samplesheet.csv
 scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
 
 
-cat <<EOF > mag_complete.sbatch
+cat <<EOF > mag_all.sbatch
 #!/bin/sh
 #SBATCH --ntasks 1
 #SBATCH --cpus-per-task 2
 #SBATCH --mem 8G
-#SBATCH --time 120:00:00
+#SBATCH --time 72:00:00
 #SBATCH --partition long_idx
-#SBATCH --output $(date '+%Y%m%d')_mag_complete.log
+#SBATCH --output $(date '+%Y%m%d')_mag_all.log
 #SBATCH --chdir $scratch_dir
 
 # module load Nextflow/23.10.0 singularity
@@ -30,8 +30,8 @@ nextflow run /data/bi/pipelines/nf-core-mag/nf-core-mag-2.5.3/workflow/main.nf \
     --input samplesheet.csv \\
     --kraken2_db '/data/bi/references/kraken/minikraken_8GB_20200312.tgz' \\
     --skip_spadeshybrid true \\
-    --outdir $(date '+%Y%m%d')_mag_complete \\
+    --outdir $(date '+%Y%m%d')_mag_all \\
     -resume
 EOF
 
-echo "sbatch mag_complete.sbatch" > _01_run_mag_complete.sh
+echo "sbatch mag_all.sbatch" > _01_run_mag_all.sh
diff --git a/bu_isciii/templates/mag/ANALYSIS/lablog_mag_all b/bu_isciii/templates/mag/ANALYSIS/lablog_mag_all
@@ -2,4 +2,4 @@ mkdir 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 ANALYSIS01_MAG_ALL $(date '+%Y%m%d')_ANALYSIS01_MAG_ALL
+mv ANALYSIS03_MAG_ALL $(date '+%Y%m%d')_ANALYSIS03_MAG_ALL
diff --git a/bu_isciii/templates/mag/DOC/mag.config b/bu_isciii/templates/mag/DOC/mag.config
@@ -43,7 +43,7 @@ process {
                 time = { 4.h * task.attempt }
 	}
 	withName:'BOWTIE2_PHIX_REMOVAL_BUILD'{
-		time = 12.h
+		time = 18.h
 	}
 }
 
@@ -52,3 +52,23 @@ params {
 	max_cpus = 32
 	max_time = '48.h'
 }
+
+/*
+    CUSTOM OUTPUT FOLDER STRUCTURE -- modules.config
+*/
+params { publish_dir_mode = 'copy' }
+process {
+	withName: 'MULTIQC' {
+        publishDir = [
+            path: { "${params.outdir}/99-stats" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> 
+				if (filename.equals('versions.yml') || filename.endsWith('.csv')) {
+                    null
+				} else {
+					filename
+                }
+            }
+		]
+	}
+}
diff --git a/bu_isciii/templates/mag/RESULTS/lablog_mag_all_results b/bu_isciii/templates/mag/RESULTS/lablog_mag_all_results
@@ -0,0 +1,6 @@
+mkdir $(date '+%Y%m%d')_entrega01
+cd $(date '+%Y%m%d')_entrega01
+
+#Create symbolic links depending on the analysis
+#Individual files
+ln -s ../../ANALYSIS/*_ANALYSIS03_MAG_ALL/99-stats/multiqc_report.html ./krona_results.html
diff --git a/.../templates/mag/RESULTS/lablog_mag_results → ...mag/RESULTS/lablog_mag_taxonomics_results b/.../templates/mag/RESULTS/lablog_mag_results → ...mag/RESULTS/lablog_mag_taxonomics_results