Merge pull request #187 from Daniel-VM/hotfix

New Bacterial Genome Assembly Template: Short, Long, and Hybrid Sequences

CHANGELOG.md

@@ -58,6 +58,7 @@ Code contributions to the hotfix:
 - [Jaime Ozaez](https://github.com/jaimeozaez)
 - [Sara Monzón](https://github.com/saramonzon)
 - [Sarai Varona](https://github.com/svarona)
+- [Daniel Valle](https://github.com/Daniel-VM)
 
 
 ### Template fixes and updates
@@ -67,6 +68,7 @@ Code contributions to the hotfix:
 - Small changes to `buisciii_tools/bu_isciii/templates/viralrecon/RESULTS/viralrecon_results` for blast and new excel_generator.py
 - Introduced better error handling in excel_generator.py. Now it can also be used for single files
 - Brought back `PASS_ONLY` to exometrio's `exomiser_configfile.yml`
+- [#187](https://github.com/BU-ISCIII/buisciii-tools/pull/187) - Added new template for bacterial assembly. Allowing for short, long and hybrid assembly.
 
 ### Modules
 

bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog

@@ -1,31 +1,97 @@
-echo "Do you want to save trimmed reads in outdir?"
+# Function to print colored text
+print_color() {
+    case "$2" in
+        "red")
+            echo -e "\e[1;31m$1\e[0m"
+            ;;
+        "green")
+            echo -e "\e[1;32m$1\e[0m"
+            ;;
+        "blue")
+            echo -e "\e[1;34m$1\e[0m"
+            ;;
+        *)
+            echo "$1"
+            ;;
+    esac
+}
 
-read -p 'Write y or n: ' trimmed
+# Function to prompt with color
+prompt_with_color() {
+    read -p "$(print_color $1 'blue') $2" response
+}
 
-TRIMMED=$(echo "${trimmed}" | tr '[:upper:]' '[:lower:]')
+# Select assembly mode
+assembly_options=("short" "long" "hybrid")
+print_color "Indicate the preferred assembly mode:" 'blue'
+select ASSEMBLY_MODE in "${assembly_options[@]}"; do
+    if [ -n "$ASSEMBLY_MODE" ]; then
+        if [ $ASSEMBLY_MODE == "short" ]; then 
+            ASSEMBLER="unicycler"
+        elif [ "$ASSEMBLY_MODE" == "long" ] || [ "$ASSEMBLY_MODE" == "hybrid" ]; then
+            ASSEMBLER="dragonflye"
+        fi
+        break
+    else
+        print_color "Invalid input. Please select a valid option." 'red'
+    fi
+done
+print_color "Selected assembly mode: $ASSEMBLY_MODE" 'green'
 
-if [ "$TRIMMED" == "yes" ] || [ "$TRIMMED" == "y" ]
-then SAVETRIMMED="True"
-else SAVETRIMMED="False"
-fi
+# Select whether to save trimmed reads
+trim_options=("Yes" "No")
+print_color "Do you want to save trimmed reads in outdir?" 'blue'
+select TRIMMED in "${trim_options[@]}"; do
+    if [ -n "$TRIMMED" ]; then
+        # rename trimmed
+        if [ "$TRIMMED" == "Yes" ] || [ "$TRIMMED" == "y" ]; then
+            SAVETRIMMED="true"
+        else 
+            SAVETRIMMED="false"
+        fi
 
-echo "Is gram positive or negative?"
+        break
+    else
+        print_color "Invalid input. Please select a valid option." 'red'
+    fi
+done
+print_color "Selected trimmed file option: $TRIMMED save trimmed" 'green'
 
-read -p 'Write + or -: ' grammtype
+# Select Prokka gram type
+gram_options=("+" "-" "skip")
 
-if [ "$grammtype" != "-" ] && [ "$grammtype" != "+" ]
-then
-    echo "The given param: $grammtype does not match any of the accepted params ('+' or '-')"
-    exit 1
-fi
+print_color "Is gram positive or negative?" 'blue'
+select GRAMTYPE in "${gram_options[@]}"; do
+    if [ -n "$GRAMTYPE" ]; then
+        if [ "$GRAMTYPE" != "skip" ]; then
+            PROKKA_ARGS="--prokka_args '--gram ${GRAMTYPE}'"
+        fi
+        break
+    else
+        print_color "Invalid input. Please select a valid option." 'red'
+    fi
+done
 
+print_color "Selected Prokka gram type: $GRAMTYPE" 'green'
+
+
+# SETUP INTPUT SAMPLE SHEET
 ln -s ../00-reads .
 ln -s ../samples_id.txt .
 
-echo "sample,fastq_1,fastq_2" > samplesheet.csv
-cat samples_id.txt | while read in; do echo "${in},00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz"; done >> samplesheet.csv
+echo "ID,R1,R2,LongFastQ,Fast5,GenomeSize" > samplesheet.csv
+cat samples_id.txt | while read in; do
+    if [ "$ASSEMBLY_MODE" == "short" ]; then
+        echo "${in},00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz,NA,NA,NA";
+    elif [ "$ASSEMBLY_MODE" == "long" ]; then
+        echo "${in},NA,NA,00-reads/${in}.fastq.gz,NA,NA";
+    elif [ "$ASSEMBLY_MODE" == "hybrid" ]; then
+        echo "${in},00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz,00-reads/${in}.fastq.gz,NA,NA";
+    else
+        echo "Format not recognized for the sample : ${in}.";
+    fi
+done >> samplesheet.csv
 
-#module load Nextflow/21.10.6 singularity
 scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
 
 cat <<EOF > assembly.sbatch
@@ -38,20 +104,28 @@ cat <<EOF > assembly.sbatch
 #SBATCH --output $(date '+%Y%m%d')_assembly01.log
 #SBATCH --chdir $scratch_dir
 
-export NXF_OPTS="-Xms500M -Xmx4G"
-
-nextflow run /scratch/bi/pipelines/BU_ISCIII-bacterial-assembly/main.nf \\
-          -c ../../DOC/hpc_slurm_assembly.config \\
-          --input samplesheet.csv \\
-          --outdir ./ \\
-          --cut_mean_quality 20 \\
-          --qualified_quality_phred 20 \\
-          --gram ${grammtype} \\
-          --reference_outdir ../../REFERENCES \\
-	  --save_trimmed ${SAVETRIMMED} \\
-          --kmerfinder_bacteria_database '/data/bi/references/kmerfinder/20190108_stable_dirs/bacteria' \\
-          --reference_ncbi_bacteria '/data/bi/references/bacteria/latest_db/assembly_summary_bacteria.txt' \\
-          -resume
+# module load Nextflow/23.10.0 singularity
+export NXF_OPTS="-Xms500M -Xmx8G"
+
+nextflow run /data/bi/pipelines/nf-core-bacass/main.nf \\
+        -c ../../DOC/hpc_slurm_assembly.config \\
+        -profile singularity \\
+        --input samplesheet.csv \\
+        --outdir ./ \\
+        --assembly_type ${ASSEMBLY_MODE} \\
+        --assembler ${ASSEMBLER} \\
+        --skip_polish true \\
+        --save_trimmed ${SAVETRIMMED} \\
+        --fastp_args '--qualified_quality_phred 20 --cut_mean_quality 20' \\
+        --skip_kraken2 true \\
+        --skip_kmerfinder false \\
+        --kmerfinderdb /data/bi/references/kmerfinder/20190108_stable_dirs/bacteria \\
+        --ncbi_assembly_metadata /data/bi/references/bacteria/20191212/assembly_summary_bacteria.txt \\
+        ${PROKKA_ARGS} \\
+        -resume
+
 EOF
 
 echo "sbatch assembly.sbatch" > _01_nf_assembly.sh
+
+

bu_isciii/templates/assembly/ANALYSIS/lablog_assembly

@@ -1,4 +1,21 @@
 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 ANALYSIS01_ASSEMBLY $(date '+%Y%m%d')_ANALYSIS01_ASSEMBLY
+cd 00-reads
+
+# Loop through each file in the directory
+while IFS= read -r sample; do
+    # Extract the file name with&without extension
+    filename_noext=$(basename -s .fastq.gz ../../RAW/${sample}*)
+
+    ### Check if the file is a short read or long read
+    for fileitem in $filename_noext; do
+        if [[ "$fileitem" =~ _R[12] ]]; then
+            ln -s -f ../../RAW/${sample}*_R1*.fastq.gz ${sample}_R1.fastq.gz
+            ln -s -f ../../RAW/${sample}*_R2*.fastq.gz ${sample}_R2.fastq.gz
+        elif [[ ! "$fileitem" =~ _R[12] ]]; then
+            ln -s -f ../../RAW/${sample}.fastq.gz ${sample}.fastq.gz
+        fi
+    done
+done < ../samples_id.txt
+
+cd -
+mv ANALYSIS01_ASSEMBLY "$(date '+%Y%m%d')_ANALYSIS01_ASSEMBLY"