From c2056d18e9a7c7246032451847df934458e687d2 Mon Sep 17 00:00:00 2001
From: Martin Beracochea <mbc@ebi.ac.uk>
Date: Tue, 6 Dec 2022 15:43:14 +0000
Subject: [PATCH] Output folder fix on step8

---
 bin/run-toil.sh                | 18 +++++++++---------
 src/steps/8_post_processing.sh | 22 +++++++++++-----------
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/bin/run-toil.sh b/bin/run-toil.sh
index f8d39cf3..195b7773 100644
--- a/bin/run-toil.sh
+++ b/bin/run-toil.sh
@@ -16,7 +16,7 @@ while getopts :n:y:c:m:q:b:s:o:t:p: option; do
     q) QUEUE=${OPTARG} ;;
     s) SINGULARITY_ON=${OPTARG} ;;
     o) OUTDIR=${OPTARG} ;;
-    n) OUTDIRNAME=${OPTARG} ;;
+    n) JOB_NAME=${OPTARG} ;;
     t) TMPDIR=${OPTARG} ;;
     p) PIPELINE_DIRECTORY=${OPTARG} ;;
     *)
@@ -32,14 +32,14 @@ export TOIL_LSF_ARGS="-q ${QUEUE}"
 
 echo "${TOIL_LSF_ARGS}"
 
-export RUN_OUTDIR=${OUTDIR}/${OUTDIRNAME}
-export LOG_DIR=${OUTDIR}/logs/${OUTDIRNAME}
-export RUN_TOIL_JOBSTORE=${TOIL_JOBSTORE}/${OUTDIRNAME}
+export RUN_OUTDIR=${OUTDIR}
+export LOG_DIR=${OUTDIR}/logs/${JOB_NAME}
+export RUN_TOIL_JOBSTORE=${TOIL_JOBSTORE}/${JOB_NAME}
 
 rm -rf "${RUN_TOIL_JOBSTORE}" || true
 mkdir -p "${RUN_OUTDIR}" "${LOG_DIR}"
 
-echo "Log-file ${LOG_DIR}/${OUTDIRNAME}.log"
+echo "Log-file ${LOG_DIR}/${JOB_NAME}.log"
 
 now="$(date)"
 echo "Toil start: $now"
@@ -54,7 +54,7 @@ if [ "${SINGULARITY_ON}" == "True" ]; then
         --writeLogs "${LOG_DIR}" \
         --maxLogFileSize 50000000 \
         --outdir "${RUN_OUTDIR}" \
-        --logFile "${LOG_DIR}/${OUTDIRNAME}.log" \
+        --logFile "${LOG_DIR}/${JOB_NAME}.log" \
         --rotatingLogging \
         --singularity \
         --batchSystem lsf \
@@ -63,7 +63,7 @@ if [ "${SINGULARITY_ON}" == "True" ]; then
         --jobStore "${RUN_TOIL_JOBSTORE}" \
         --retryCount 2 \
         --defaultMemory ${MEMORY} \
-        "${CWL}" "${YML}" >"${LOG_DIR}/${OUTDIRNAME}.json"
+        "${CWL}" "${YML}" >"${LOG_DIR}/${JOB_NAME}.json"
 else
     toil-cwl-runner \
         --logWarning \
@@ -72,7 +72,7 @@ else
         --writeLogs "${LOG_DIR}" \
         --maxLogFileSize 50000000 \
         --outdir "${RUN_OUTDIR}" \
-        --logFile "${LOG_DIR}/${OUTDIRNAME}.log" \
+        --logFile "${LOG_DIR}/${JOB_NAME}.log" \
         --rotatingLogging \
         --no-container --preserve-entire-environment \
         --batchSystem lsf \
@@ -81,7 +81,7 @@ else
         --jobStore "${RUN_TOIL_JOBSTORE}" \
         --retryCount 2 \
         --defaultMemory ${MEMORY} \
-        "${CWL}" "${YML}" >"${LOG_DIR}/${OUTDIRNAME}.json"
+        "${CWL}" "${YML}" >"${LOG_DIR}/${JOB_NAME}.json"
 fi
 
 now="$(date)"
diff --git a/src/steps/8_post_processing.sh b/src/steps/8_post_processing.sh
index 913e9d09..55b7638b 100755
--- a/src/steps/8_post_processing.sh
+++ b/src/steps/8_post_processing.sh
@@ -99,11 +99,11 @@ bsub \
     -e "${LOGS}"/"${JOB}".post-processing.yml.err \
     -o "${LOGS}"/"${JOB}".post-processing.yml.out \
     bash "${PIPELINE_DIRECTORY}"/src/steps/8_generate_yml.sh \
-    -b "${BIOM}" \
-    -m "${METADATA}" \
-    -y "${YML_FILE}" \
-    -o "${OUT}" \
-    -a "${ANNOTATIONS}"
+        -b "${BIOM}" \
+        -m "${METADATA}" \
+        -y "${YML_FILE}" \
+        -o "${OUT}" \
+        -a "${ANNOTATIONS}"
 
 CWL="${PIPELINE_DIRECTORY}"/src/cwl/sub-wfs/wf-6-post-processing.cwl
 
@@ -118,9 +118,9 @@ bsub \
     -M "${MEM}" \
     -n "${THREADS}" \
     bash "${PIPELINE_DIRECTORY}"/bin/run-toil.sh \
-    -n "${DIRNAME}_metadata" \
-    -q "${QUEUE}" \
-    -p "${PIPELINE_DIRECTORY}" \
-    -o "${OUT}" \
-    -c "${CWL}" \
-    -y "${YML_FILE}"
+        -n "${DIRNAME}_metadata" \
+        -q "${QUEUE}" \
+        -p "${PIPELINE_DIRECTORY}" \
+        -o "${OUT}" \
+        -c "${CWL}" \
+        -y "${YML_FILE}"