Modified pipelines paths where necessary

BU-ISCIII · Jun 18, 2024 · 97c08fe · 97c08fe
1 parent 9eb9f21
commit 97c08fe
Show file tree

Hide file tree

Showing 13 changed files with 17 additions and 17 deletions.
diff --git a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog
@@ -5,7 +5,7 @@ mkdir logs
 
 scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
 
-cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --cpus-per-task 32 --mem 35000M --chdir $scratch_dir --time 01:00:00 --output logs/IRMA.${in}.%j.log /data/bi/pipelines/flu-amd-202402/IRMA FLU_AD ../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz ${in} --external-config ../../../DOC/irma_config.sh &"; done > _01_irma.sh
+cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --cpus-per-task 32 --mem 35000M --chdir $scratch_dir --time 01:00:00 --output logs/IRMA.${in}.%j.log /data/bi/pipelines/flu-amd/flu-amd-1.1.4/IRMA FLU_AD ../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz ${in} --external-config ../../../DOC/irma_config.sh &"; done > _01_irma.sh
 
 echo 'bash create_irma_stats.sh' > _02_create_stats.sh
 
@@ -32,4 +32,4 @@ echo 'grep -w 'C__' irma_stats.txt | cut -f1 | while read sample; do cat C_fragm
 echo 'cat ../samples_id.txt | while read in; do cat ${in}/*.fasta | sed "s/^>/\>${in}_/g" | sed 's/_H1//g' | sed 's/_H3//g' | sed 's/_N1//g' | sed 's/_N2//g' | sed 's@-@/@g' | sed 's/_A_/_/g' | sed 's/_B_/_/g' | sed 's/_C_/_/g' >> all_samples_completo.txt; done' >> _03_post_processing.sh
 
 echo 'sed "s/__//g" irma_stats.txt > clean_irma_stats.txt' >> _03_post_processing.sh
-echo 'sed "s/_\t/\t/g" irma_stats.txt > clean_irma_stats.txt' >> _03_post_processing.sh
+echo 'sed "s/_\t/\t/g" irma_stats.txt > clean_irma_stats.txt' >> _03_post_processing.sh
diff --git a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS02_MET/lablog b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS02_MET/lablog
@@ -18,7 +18,7 @@ cat <<EOF > mag.sbatch
 
 export NXF_OPTS="-Xms500M -Xmx4G"
 
-nextflow run /scratch/bi/pipelines/nf-core-mag-2.1.1/workflow/main.nf \\
+nextflow run /data/bi/pipelines/nf-core-mag/nf-core-mag-2.1.1/workflow/main.nf \\
           -c ../../DOC/mag.config \\
           --input '00-reads/*_R{1,2}.fastq.gz' \\
           --outdir $(date '+%Y%m%d')_mag \\

diff --git a/bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog b/bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog
@@ -107,7 +107,7 @@ cat <<EOF > assembly.sbatch
 # module load Nextflow/23.10.0 singularity
 export NXF_OPTS="-Xms500M -Xmx8G"
 
-nextflow run /data/bi/pipelines/nf-core-bacass/main.nf \\
+nextflow run /data/bi/pipelines/nf-core-bacass/nf-core-bacass-2.2.0dev/main.nf \\
         -c ../../DOC/hpc_slurm_assembly.config \\
         -profile singularity \\
         --input samplesheet.csv \\

diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/lablog
@@ -17,7 +17,7 @@ cat <<EOF > mag.sbatch
 
 export NXF_OPTS="-Xms500M -Xmx4G"
 
-nextflow run /scratch/bi/pipelines/nf-core-mag-2.1.1/workflow/main.nf \\
+nextflow run /data/bi/pipelines/nf-core-mag/nf-core-mag-2.1.1/workflow/main.nf \\
           -c ../../DOC/mag.config \\
           --input '00-reads/*_R{1,2}.fastq.gz' \\
           --outdir $(date '+%Y%m%d')_mag \\

diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/07-annotation/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/07-annotation/lablog
@@ -27,7 +27,7 @@ echo "sbatch bcftools_query.sbatch" > _01_bcftools_query.sh
 
 
 # module load Java/1.8.0_281 R/4.1.0-foss-2021a
-cat ../samples_id.txt | xargs -I @@ echo "mkdir @@;srun --chdir ${scratch_dir} --output logs/KGGSEQ.@@.%j.log --job-name KGGSEQ --cpus-per-task 1 --mem 8192 --partition short_idx --time 02:00:00 java -jar -Xmx8g /data/bi/pipelines/kggseqhg19/kggseq.jar --no-web --buildver hg19 --vcf-file ../06-VarScan/@@/@@.vcf.gz --db-gene refgene --db-score dbnsfp --genome-annot --db-filter ESP5400,dbsnp141,1kg201305 --rare-allele-freq 1 --mendel-causing-predict best --omim-annot --out @@/@@_annot.txt --no-qc &" > _02_kggseq.sh
+cat ../samples_id.txt | xargs -I @@ echo "mkdir @@;srun --chdir ${scratch_dir} --output logs/KGGSEQ.@@.%j.log --job-name KGGSEQ --cpus-per-task 1 --mem 8192 --partition short_idx --time 02:00:00 java -jar -Xmx8g /data/bi/pipelines/kggseq/kggseqhg19/kggseq.jar --no-web --buildver hg19 --vcf-file ../06-VarScan/@@/@@.vcf.gz --db-gene refgene --db-score dbnsfp --genome-annot --db-filter ESP5400,dbsnp141,1kg201305 --rare-allele-freq 1 --mendel-causing-predict best --omim-annot --out @@/@@_annot.txt --no-qc &" > _02_kggseq.sh
 cat ../samples_id.txt | xargs -I % echo "gunzip %/%_annot.txt.flt.txt.gz" > _03_final_table.sh
 cat ../samples_id.txt | xargs -I % echo 'cp header %/%_header.table && tail -n +2 %/%.table >> %/%_header.table'  >> _03_final_table.sh
 cat ../samples_id.txt | xargs -I % echo "Rscript merge_parse.R %" >> _03_final_table.sh

diff --git a/bu_isciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/02-kmerfinder/lablog b/bu_isciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/02-kmerfinder/lablog
@@ -4,7 +4,7 @@ scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
 
 mkdir logs
 
-cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --chdir ${scratch_dir} --mem 50G --output logs/KMERFINDER.${in}.%j.log singularity run -B /scratch/bi/ -B /data/bi/references/kmerfinder/20190108_stable_dirs/bacteria /scratch/bi/pipelines/kmerfinder_v3.0.simg -i ../01-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../01-preprocessing/${in}/${in}_R2_filtered.fastq.gz -o ${scratch_dir}/${in} -db /data/bi/references/kmerfinder/20190108_stable_dirs/bacteria/bacteria.ATG -tax /data/bi/references/kmerfinder/20190108_stable_dirs/bacteria/bacteria.name -x &";done > _01_kmerfinder.sh
+cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --chdir ${scratch_dir} --mem 50G --output logs/KMERFINDER.${in}.%j.log singularity run -B /scratch/bi/ -B /data/bi/references/kmerfinder/20190108_stable_dirs/bacteria /data/bi/pipelines/singularity-images/kmerfinder_v3.0.simg -i ../01-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../01-preprocessing/${in}/${in}_R2_filtered.fastq.gz -o ${scratch_dir}/${in} -db /data/bi/references/kmerfinder/20190108_stable_dirs/bacteria/bacteria.ATG -tax /data/bi/references/kmerfinder/20190108_stable_dirs/bacteria/bacteria.name -x &";done > _01_kmerfinder.sh
 
 echo "cat ../samples_id.txt | xargs -I % awk '{FS=\"\t\"} NR==2 {print \$1}' %/results.txt | awk '{count[\$0]++} END{for (i in count) {print count[i], i}}' | sort -nr" > _02_find_common_reference.sh
 

diff --git a/bu_isciii/templates/pikavirus/ANALYSIS/ANALYSIS01_PIKAVIRUS/lablog b/bu_isciii/templates/pikavirus/ANALYSIS/ANALYSIS01_PIKAVIRUS/lablog
@@ -20,7 +20,7 @@ cat <<EOF > pikavirus.sbatch
 
 export NXF_OPTS="-Xms500M -Xmx4G"
 
-nextflow run /scratch/bi/pipelines/PikaVirus/main.nf \\
+nextflow run /data/bi/pipelines/pikavirus/PikaVirus/main.nf \\
           -c ../../DOC/hpc_slurm_pikavirus.config \\
           --input samplesheet.csv \\
           --kraken_scouting false \\

diff --git a/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog b/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog
@@ -19,7 +19,7 @@ cat <<EOF > rnaseq.sbatch
 
 export NXF_OPTS="-Xms500M -Xmx4G"
 
-/data/bi/pipelines/nf-core-rnaseq-3.10.1/workflow/main.nf \\
+/data/bi/pipelines/nf-core-rnaseq/nf-core-rnaseq-3.10.1/workflow/main.nf \\
           -c ../../DOC/hpc_slurm_rnaseq.config \\
           -params-file ../../DOC/hg38_ensmbl_rnaseq.yml \\
           --input samplesheet.csv \\

diff --git a/bu_isciii/templates/seek_and_destroy/ANALYSIS/ANALYSIS01_SEEK_DESTROY/lablog b/bu_isciii/templates/seek_and_destroy/ANALYSIS/ANALYSIS01_SEEK_DESTROY/lablog
@@ -21,7 +21,7 @@ cat <<EOF > seek_destroy.sbatch
 
 export NXF_OPTS="-Xms500M -Xmx4G"
 
-nextflow run /scratch/bi/pipelines/Seek-Destroy/main.nf  \\
+nextflow run /data/bi/pipelines/seek-destroy-nf/main.nf  \\
           -c ../../DOC/seek_destroy.config \\
           --input samplesheet.csv \\
 	  --scout_database /data/bi/references/kraken/minikraken_8GB_20200312.tgz \\

diff --git a/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon b/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon
@@ -363,7 +363,7 @@ do
         echo "#SBATCH --output ${ref}_$(date '+%Y%m%d')_viralrecon.log" >> ${FOLDER_NAME}/lablog
         printf "#SBATCH --chdir \$scratch_dir\n\n" >> ${FOLDER_NAME}/lablog
         printf 'export NXF_OPTS="-Xms500M -Xmx4G"\n\n' >> ${FOLDER_NAME}/lablog
-        echo "nextflow run /data/bi/pipelines/nf-core-viralrecon-2.6.0/workflow/main.nf \\\\" >> ${FOLDER_NAME}/lablog
+        echo "nextflow run /data/bi/pipelines/nf-core-viralrecon/nf-core-viralrecon-2.6.0/workflow/main.nf \\\\" >> ${FOLDER_NAME}/lablog
         echo "          -c ../${CONFIG_FILE} \\\\" >> ${FOLDER_NAME}/lablog
         echo "          -params-file ../${PARAMS_FILE} \\\\" >> ${FOLDER_NAME}/lablog
         echo "          --input samplesheet_${ref}.csv \\\\" >> ${FOLDER_NAME}/lablog
@@ -404,4 +404,4 @@ rm _02_create_run_percentage_Ns.sh
 mv DATE_ANALYSIS0X_MAG $(date '+%Y%m%d')_ANALYSIS0X_MAG
 cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R1*.fastq.gz %_R1.fastq.gz" | bash; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R2*.fastq.gz %_R2.fastq.gz" | bash; cd ..
 
-echo_green "\nLablog_viralrecon execution has been completed successfully!"
+echo_green "\nLablog_viralrecon execution has been completed successfully!"
diff --git a/bu_isciii/templates/viralrecon/DOC/viralrecon.config b/bu_isciii/templates/viralrecon/DOC/viralrecon.config
@@ -1,7 +1,7 @@
 singularity {
 	enabled = true
 	autoMounts = true
-        runOptions = '-B /data/bi/references/ -B /data/bi/pipelines/artic-ncov2019/ -B "$HOME"'
+        runOptions = '-B /data/bi/references/ -B /data/bi/pipelines/artic-ncov2019/artic-ncov2019/ -B "$HOME"'
 }
 
 process {

diff --git a/bu_isciii/templates/viralrecon/DOC/viralrecon_sars_nanopore.config b/bu_isciii/templates/viralrecon/DOC/viralrecon_sars_nanopore.config
@@ -1,7 +1,7 @@
 singularity {
 	enabled = true
 	autoMounts = true
-        runOptions = '-B /data/bi/references/ -B /data/bi/pipelines/artic-ncov2019/'
+        runOptions = '-B /data/bi/references/ -B /data/bi/pipelines/artic-ncov2019/artic-ncov2019/'
 }
 
 process {
@@ -10,7 +10,7 @@ process {
         withName: 'ARTIC_MINION' {
             ext.args = [
                 '--normalise 500',
-                '--scheme-directory /data/bi/pipelines/artic-ncov2019/primer_schemes/',
+                '--scheme-directory /data/bi/pipelines/artic-ncov2019/artic-ncov2019/primer_schemes/',
                 '--medaka'
             ].join(' ').trim()
         }

diff --git a/bu_isciii/templates/viralrecon/DOC/viralrecon_sars_nanopore_params.yml b/bu_isciii/templates/viralrecon/DOC/viralrecon_sars_nanopore_params.yml
@@ -2,8 +2,8 @@ platform: 'nanopore'
 protocol: 'amplicon'
 artic_scheme: 'nCoV-2019'
 primer_set_version: 5
-fasta: '/data/bi/pipelines/artic-ncov2019/primer_schemes/nCoV-2019/V5/ESIB-EQA.reference.fasta'
-primer_bed: '/data/bi/pipelines/artic-ncov2019/primer_schemes/nCoV-2019/V5/ESIB-EQA.primer.bed'
+fasta: '/data/bi/pipelines/artic-ncov2019/artic-ncov2019/primer_schemes/nCoV-2019/V5/ESIB-EQA.reference.fasta'
+primer_bed: '/data/bi/pipelines/artic-ncov2019/artic-ncov2019/primer_schemes/nCoV-2019/V5/ESIB-EQA.primer.bed'
 primer_fasta: '../../RAW/ESIB_EQA_2023.SARS1/ESIB_EQA_2023.SARS1.primers.fasta'
 kraken2_db: '/data/bi/references/eukaria/homo_sapiens/hg38/UCSC/kraken2/kraken2_human.tar.gz'
 nextclade_dataset_name: 'sars-cov-2'