diff --git a/CHANGELOG.md b/CHANGELOG.md index ecfd10de..77b146ea 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -44,7 +44,8 @@ Code contributions to the new version: - Included annotated tab description in exome-trios markdowns [#273](https://github.com/BU-ISCIII/buisciii-tools/pull/273) - Installed all necessary singularity images and modified all templates so that, instead of using conda environments or loaded modules, the corresponding singularity images are used [#272](https://github.com/BU-ISCIII/buisciii-tools/pull/272) - Updated sarek version in exomeeb, exometrio and wgstrio templates [#277](https://github.com/BU-ISCIII/buisciii-tools/pull/277) -- Extension file of all_samples_virus_table_filtered (from csv to tsv) in lablog_viralrecon_results changed [#278](https://github.com/BU-ISCIII/buisciii-tools/pull/278) +- Extension file of all_samples_virus_table_filtered (from csv to tsv) in lablog_viralrecon_results changed [#278](https://github.com/BU-ISCIII/buisciii-tools/pull/278) +- Fixed singularity-images path when updating pangolin database in lablog_viralrecon. Added line break after prompted input. [#282](https://github.com/BU-ISCIII/buisciii-tools/pull/282) ### Modules diff --git a/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon b/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon index 58fa2170..916f3d7f 100644 --- a/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon +++ b/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon @@ -65,10 +65,10 @@ update_pangolin() { echo -e "Pangolin database is UP TO DATE. \xE2\x9C\x85" else mkdir "$(date '+%Y%m%d')" - srun --partition short_idx singularity run -B ${PWD} /scratch/bi/singularity-images/$latest_version_pangolin pangolin --update-data --datadir ${PWD}/$(date '+%Y%m%d')/ + srun --partition short_idx singularity run -B ${PWD} /data/bi/pipelines/singularity-images/$latest_version_pangolin pangolin --update-data --datadir ${PWD}/$(date '+%Y%m%d')/ # log file creation echo -e "$(date +'%Y-%m-%d %H:%M:%S')\tmkdir $(date '+%Y%m%d')" >> $(date '+%Y%m%d')/log - echo -e "$(date +'%Y-%m-%d %H:%M:%S')\tsrun --partition short_idx singularity run -B ${PWD} /scratch/bi/singularity-images/$latest_version_pangolin pangolin --update-data --datadir ${PWD}/$(date '+%Y%m%d')/)" >> $(date '+%Y%m%d')/log + echo -e "$(date +'%Y-%m-%d %H:%M:%S')\tsrun --partition short_idx singularity run -B ${PWD} /data/bi/pipelines/singularity-images/$latest_version_pangolin pangolin --update-data --datadir ${PWD}/$(date '+%Y%m%d')/)" >> $(date '+%Y%m%d')/log echo_green "Pangolin database UPDATED." fi cd - @@ -211,7 +211,7 @@ echo_bold "\nPlease specify the type of analysis." echo_bold "1. METAGENOMICS" echo_bold "2. AMPLICONS" while true; do - echo -ne "\e[1;38;5;220m"; read -n 1 ANALYSIS_TYPE; tput sgr0 + echo -ne "\e[1;38;5;220m"; read -n 1 ANALYSIS_TYPE; tput sgr0; echo if [ "$ANALYSIS_TYPE" == "1" ]; then ANALYSIS_TYPE="METAGENOMIC" echo_green "$ANALYSIS_TYPE analysis selected." @@ -230,7 +230,7 @@ echo_bold "\nPlease specify the method to be performed." echo_bold "2. De novo assemby" echo_bold "3. Both" while true; do - echo -ne "\e[1;38;5;220m"; read -n 1 method; tput sgr0 + echo -ne "\e[1;38;5;220m"; read -n 1 method; tput sgr0; echo if [ "$method" == "1" ]; then echo_green "Mapping method selected." break @@ -251,7 +251,7 @@ echo_bold "\nPlease specify the method to be performed." # Setting samples_ref.txt file echo -read -p $'\e[1;37mIs samples_ref.txt file already prepared? [y/N]: \e[1;38;5;220m' -n 1 samples_ref_prepared; tput sgr0 +read -p $'\e[1;37mIs samples_ref.txt file already prepared? [y/N]: \e[1;38;5;220m' -n 1 samples_ref_prepared; tput sgr0; echo if [ "$samples_ref_prepared" == "y" ]; then echo -e "File samples_ref.txt READY. \xE2\x9C\x85" else @@ -260,7 +260,7 @@ else while [ -z "$host" ] || [ -z "$reference" ] || [ "$answer" = "n" ]; do read -p $'\e[1;37mPlease specify the host: \e[1;38;5;220m' host read -p $'\e[1;37mPlease specify the reference: \e[1;38;5;220m' reference - read -p $'\e[1;37mAre host [\e[1;38;5;220m'"${host^^}"$'\e[1;37m] and reference [\e[1;38;5;220m'"${reference}"$'\e[1;37m] correct? [Y/n]: \e[1;38;5;220m' -n 1 answer; tput sgr0 + read -p $'\e[1;37mAre host [\e[1;38;5;220m'"${host^^}"$'\e[1;37m] and reference [\e[1;38;5;220m'"${reference}"$'\e[1;37m] correct? [Y/n]: \e[1;38;5;220m' -n 1 answer; tput sgr0; echo done while read in; do echo -e "${in}\t${reference}\t${host^^}" >> samples_ref.txt; done < samples_id.txt echo -e "File samples_ref.txt READY. \xE2\x9C\x85" @@ -272,7 +272,7 @@ if [ "$ANALYSIS_TYPE" = "METAGENOMIC" ]; then # Nextclade is able to analyze monkeypox virus echo - read -p $'\e[1;37mDo the sequences correspond to monkeypox virus (MPV)? [y/N]: \e[1;38;5;220m' -n 1 monkeypox; tput sgr0 + read -p $'\e[1;37mDo the sequences correspond to monkeypox virus (MPV)? [y/N]: \e[1;38;5;220m' -n 1 monkeypox; tput sgr0; echo if [ "$monkeypox" == "y" ]; then virus_tag='mpox' @@ -291,7 +291,7 @@ else echo_bold "2. RSV" echo_bold "3. Other" while true; do - echo -ne "\e[1;38;5;220m"; read -n 1 virus_tag; tput sgr0 + echo -ne "\e[1;38;5;220m"; read -n 1 virus_tag; tput sgr0; echo if [ "$virus_tag" == "1" ]; then virus_tag="sars-cov-2" echo_green "${virus_tag^^} virus selected."