Fixed bug with not finding juno_call.txt (wrong placement of line of …

…code)
RIVM-bioinformatics · Feb 5, 2021 · 911a47a · 911a47a
1 parent ad3663f
commit 911a47a
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Showing 3 changed files with 8 additions and 10 deletions.
diff --git a/bin/include/Clean b/bin/include/Clean
@@ -2,7 +2,7 @@
 # shellcheck disable=SC1091
 
 #############################################################
-##		Modified from Jovian			   ##
+##		Modified from Jovian			                   ##
 #############################################################
 
 should_i_clean="no"
@@ -35,21 +35,19 @@ if [ "${should_i_clean}" == "no" ]; then
 fi
 
 if [ "${should_i_clean}" == "yes" ]; then
-    echo -e "Removing Juno pipeline output: \nout/\nout/log/\nprofile/variables.yaml\nsample_sheet.yaml\n\n"
+    echo -e "Removing Juno pipeline output: \n"${OUTPUT_DIR}"/\n"${OUTPUT_DIR}"/log/\nprofile/variables.yaml\nprofile/juno_call.txt\nsample_sheet.yaml\n\n"
 
-    #@ remove the folders through a forloop with spinner + finish signal
     a=(
-    "out/"
+    "${OUTPUT_DIR}"
     "sample_sheet.yaml"
     "profile/variables.yaml"
+    "profile/juno_call.txt"
     )
 
     for i in "${a[@]}"; do
-        #start_spinner 
         echo "Removing \"${i}\""
         sleep 0.2
         rm -rf "${i}"
-        #stop_spinner $?
     done
 
 fi
diff --git a/juno b/juno
@@ -293,18 +293,18 @@ if [ -e sample_sheet.yaml ]; then
     echo -e "Server_host:\n    hostname: http://${SET_HOSTNAME}" >> profile/variables.yaml
     eval $(parse_yaml profile/variables.yaml "config_")
     if [ $LOCAL == "TRUE" ]; then
-        snakemake --config checkm=$CHECKM out=$OUTPUT_DIR genus=$GENUS_ALL metadata=$METADATA --profile profile ${@}
         echo -e "Juno call (this settings would overwrite any others in the configuration files): \n" > profile/juno_call.txt
         echo -e "snakemake --config checkm=$CHECKM out=$OUTPUT_DIR genus=$GENUS_ALL metadata=$METADATA \
 --profile profile \
 ${@} \n" >> profile/juno_call.txt
+        snakemake --config checkm=$CHECKM out=$OUTPUT_DIR genus=$GENUS_ALL metadata=$METADATA --profile profile ${@}
     else
-        snakemake --config checkm=$CHECKM out=$OUTPUT_DIR genus=$GENUS_ALL metadata=$METADATA --profile profile --drmaa " -q bio -n {threads} -R \"span[hosts=1]\"" --drmaa-log-dir ${OUTPUT_DIR}/log/drmaa ${@}
         echo -e "Juno call (this settings would overwrite any others in the configuration files): \n" > profile/juno_call.txt
         echo -e "snakemake --config checkm=$CHECKM out=$OUTPUT_DIR genus=$GENUS_ALL metadata=$METADATA \
 --profile profile \
 --drmaa  -q bio -n {threads} -R \'span[hosts=1]\'' \
 --drmaa-log-dir ${OUTPUT_DIR}/log/drmaa ${@} \n" >> profile/juno_call.txt
+        snakemake --config checkm=$CHECKM out=$OUTPUT_DIR genus=$GENUS_ALL metadata=$METADATA --profile profile --drmaa " -q bio -n {threads} -R \"span[hosts=1]\"" --drmaa-log-dir ${OUTPUT_DIR}/log/drmaa ${@}
     fi
     #echo -e "\nUnique identifier for this run is: $config_run_identifier "
     echo -e "Juno run complete"

diff --git a/justjuno.sh b/justjuno.sh
@@ -47,18 +47,18 @@ echo -e "pipeline_run:\n    identifier: ${UNIQUE_ID}" > profile/variables.yaml
 echo -e "Server_host:\n    hostname: http://${SET_HOSTNAME}" >> profile/variables.yaml
 
 if [ -z $METADATA ]; then
-    snakemake --config checkm=$CHECKM out=$OUTPUT_DIR genus=$GENUS_ALL --profile profile --drmaa " -q bio -n {threads} -R \"span[hosts=1]\"" --drmaa-log-dir ${OUTPUT_DIR}/log/drmaa
     echo -e "Juno call (this settings would overwrite any others in the configuration files): \n" > profile/juno_call.txt
     echo -e "snakemake --config checkm=$CHECKM out=$OUTPUT_DIR genus=$GENUS_ALL \
 --profile profile \
 --drmaa ' -q bio -n {threads} -R \'span[hosts=1]\'' \
 --drmaa-log-dir ${OUTPUT_DIR}/log/drmaa \
 ${@}\n" >> profile/juno_call.txt
+    snakemake --config checkm=$CHECKM out=$OUTPUT_DIR genus=$GENUS_ALL --profile profile --drmaa " -q bio -n {threads} -R \"span[hosts=1]\"" --drmaa-log-dir ${OUTPUT_DIR}/log/drmaa
 else
     echo "This is the genus file: $METADATA"
-    snakemake --config checkm=$CHECKM out=$OUTPUT_DIR genus=$GENUS_ALL metadata=$METADATA --profile profile --drmaa " -q bio -n {threads} -R \"span[hosts=1]\"" --drmaa-log-dir ${OUTPUT_DIR}/log/drmaa
     echo -e "Juno call (this settings would overwrite any others in the configuration files): \n" > profile/juno_call.txt
     echo -e "snakemake --config checkm=$CHECKM out=$OUTPUT_DIR genus=$GENUS_ALL metadata=$METADATA --profile profile \
 --drmaa  -q bio -n {threads} -R \'span[hosts=1]\'' \
 --drmaa-log-dir ${OUTPUT_DIR}/log/drmaa ${@} \n" >> profile/juno_call.txt
+    snakemake --config checkm=$CHECKM out=$OUTPUT_DIR genus=$GENUS_ALL metadata=$METADATA --profile profile --drmaa " -q bio -n {threads} -R \"span[hosts=1]\"" --drmaa-log-dir ${OUTPUT_DIR}/log/drmaa
 fi