fix: fix run_pipeline.sh

run_pipeline.sh

@@ -2,18 +2,29 @@
 
 set -euo pipefail
 
+set -x
+
 #----------------------------------------------#
 # User parameters
-if [ ! -z "${1}" ] || [ ! -z "${2}" ] #|| [ ! -z "${irods_input_projectID}" ]
+if [ ! -z "${1}" ] || [ ! -z "${2}" ] || [ ! -z "${irods_input_projectID}" ]
 then
    input_dir="${1}"
    output_dir="${2}"
-#    PROJECT_NAME="${irods_input_projectID}"
+   PROJECT_NAME="${irods_input_projectID}"
+   EXCLUSION_FILE=""
 else
     echo "One of the parameters is missing, make sure there is an input directory, output directory and project name(param 1, 2 or irods_input_projectID)."
     exit 1
 fi
 
+set +u
+#check if there is an exclusion file, if so change the parameter
+if [ ! -z "${irods_input_sequencing__run_id}" ] && [ -f "/data/BioGrid/NGSlab/sample_sheets/${irods_input_sequencing__run_id}.exclude" ]
+then
+  EXCLUSION_FILE="/data/BioGrid/NGSlab/sample_sheets/${irods_input_sequencing__run_id}.exclude"
+fi
+set -u
+
 if [ ! -d "${input_dir}" ] || [ ! -d "${output_dir}" ]
 then
   echo "The input directory $input_dir, output directory $output_dir or fastq dir ${input_dir}/clean_fastq does not exist"
@@ -23,29 +34,50 @@ else
 fi
 
 #----------------------------------------------#
-# Create/update necessary environments
-PATH_MAMBA_YAML="envs/mamba.yaml"
-PATH_MASTER_YAML="envs/juno_variant_typing.yaml"
-MAMBA_NAME=$(head -n 1 ${PATH_MAMBA_YAML} | cut -f2 -d ' ')
-MASTER_NAME=$(head -n 1 ${PATH_MASTER_YAML} | cut -f2 -d ' ')
+## make sure conda works
 
-echo -e "\nUpdating necessary environments to run the pipeline..."
-
-# Removing strict mode because it sometimes breaks the code for 
-# activating an environment and for testing whether some variables
-# are set or not
-set +euo pipefail 
+# >>> conda initialize >>>
+# !! Contents within this block are managed by 'conda init' !!
+__conda_setup="$('/mnt/miniconda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
+if [ $? -eq 0 ]; then
+    eval "$__conda_setup"
+else
+    if [ -f "/mnt/miniconda/etc/profile.d/conda.sh" ]; then
+        . "/mnt/miniconda/etc/profile.d/conda.sh"
+    else
+        export PATH="/mnt/miniconda/bin:$PATH"
+    fi
+fi
+unset __conda_setup
+# <<< conda initialize <<<export -f conda
+export -f __conda_activate
+export -f __conda_reactivate
+export -f __conda_hashr
 
-conda env update -f "${PATH_MAMBA_YAML}"
-source activate "${MAMBA_NAME}"
 
-mamba env update -f "${PATH_MASTER_YAML}"
+#----------------------------------------------#
+# Create the environment
 
-source activate "${MASTER_NAME}"
+# we can use the base installation of mamba to create the environment. 
+# Swapping to a parent env is not necessary anymore.
+mamba env create -f envs/juno_variant_typing.yaml --name pipeline_env
+conda activate pipeline_env
 
 #----------------------------------------------#
 # Run the pipeline
 
+case $PROJECT_NAME in
+  adhoc)
+    SPECIES="NotProvided"
+    ;;
+  myco|myco_kncv)
+    SPECIES="Mycobacterium_tuberculosis"
+    ;;
+  *)
+    SPECIES="NotProvided"
+    ;;
+esac
+
 echo -e "\nRun pipeline..."
 
 if [ ! -z ${irods_runsheet_sys__runsheet__lsf_queue} ]; then
@@ -54,9 +86,32 @@ else
     QUEUE="bio"
 fi
 
-set -euo pipefail
+# Setting up the tmpdir for singularity as the current directory (default is /tmp but it gets full easily)
+# Containers will use it for storing tmp files when building a container
+export SINGULARITY_TMPDIR="$(pwd)"
 
-python template.py --queue "${QUEUE}" -i "${input_dir}" -o "${output_dir}"
+#without exclusion file
+if [ "${EXCLUSION_FILE}" == "" ]
+then
+    python juno_variant_typing.py \
+        --queue "${QUEUE}" \
+        -i "${input_dir}" \
+        -o "${output_dir}" \
+        -s "${SPECIES}" \
+        --prefix "/mnt/db/juno/sing_containers"
+
+        result=$?
+else
+    python juno_variant_typing.py \
+        --queue "${QUEUE}" \
+        -i "${input_dir}" \
+        -o "${output_dir}" \
+        -s "${SPECIES}" \
+        --prefix "/mnt/db/juno/sing_containers" \
+        -ex "${EXCLUSION_FILE}"
+
+        result=$?
+fi
 
 result=$?