From e63662489aff80e4c211e601f5f6d8312762905d Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 28 Nov 2024 03:59:51 -0800
Subject: [PATCH] Quote paths in Nextflow script to handle spaces

---
 runscripts/nextflow/analysis.nf | 20 ++++++++++----------
 runscripts/nextflow/sim.nf      |  4 ++--
 runscripts/nextflow/template.nf | 12 ++++++------
 3 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/runscripts/nextflow/analysis.nf b/runscripts/nextflow/analysis.nf
index 604d30890..53e10a4c7 100644
--- a/runscripts/nextflow/analysis.nf
+++ b/runscripts/nextflow/analysis.nf
@@ -24,8 +24,8 @@ process analysisSingle {
         --lineage_seed $lineage_seed \\
         --generation $generation \\
         --agent_id "$agent_id" \\
-        --variant_metadata_path ${variant_metadata} \\
-        -o \$(pwd)/plots \\
+        --variant_metadata_path "${variant_metadata}" \\
+        -o "\$(pwd)/plots" \\
         -t single
     cd plots
     cd experiment_id=*
@@ -71,8 +71,8 @@ process analysisMultiDaughter {
         --variant $variant \\
         --lineage_seed $lineage_seed \\
         --generation $generation \\
-        --variant_metadata_path ${variant_metadata} \\
-        -o \$(pwd)/plots \\
+        --variant_metadata_path "${variant_metadata}" \\
+        -o "\$(pwd)/plots" \\
         -t multidaughter
     cd plots
     cd experiment_id=*
@@ -116,8 +116,8 @@ process analysisMultiGeneration {
         --experiment_id "$experiment_id" \\
         --variant $variant \\
         --lineage_seed $lineage_seed \\
-        --variant_metadata_path ${variant_metadata} \\
-        -o \$(pwd)/plots \\
+        --variant_metadata_path "${variant_metadata}" \\
+        -o "\$(pwd)/plots" \\
         -t multigeneration
     cd plots
     cd experiment_id=*
@@ -159,8 +159,8 @@ process analysisMultiSeed {
         --validation_data_path "$kb/validationData.cPickle" \\
         --experiment_id "$experiment_id" \\
         --variant $variant \\
-        --variant_metadata_path ${variant_metadata} \\
-        -o \$(pwd)/plots \\
+        --variant_metadata_path "${variant_metadata}" \\
+        -o "\$(pwd)/plots" \\
         -t multiseed
     cd plots
     cd experiment_id=*
@@ -199,8 +199,8 @@ process analysisMultiVariant {
         --validation_data_path "$kb/validationData.cPickle" \\
         --experiment_id "$experiment_id" \\
         --variant ${variant.join(" ")} \\
-        --variant_metadata_path ${variant_metadata} \\
-        -o \$(pwd)/plots \\
+        --variant_metadata_path "${variant_metadata}" \\
+        -o "\$(pwd)/plots" \\
         -t multivariant
     cd plots
     cd experiment_id=*
diff --git a/runscripts/nextflow/sim.nf b/runscripts/nextflow/sim.nf
index 48b44745e..d1d3968a3 100644
--- a/runscripts/nextflow/sim.nf
+++ b/runscripts/nextflow/sim.nf
@@ -29,7 +29,7 @@ process simGen0 {
     PYTHONPATH=${params.projectRoot} python ${params.projectRoot}/ecoli/experiments/ecoli_master_sim.py \\
         --config $config \\
         --sim_data_path $sim_data \\
-        --daughter_outdir \$(pwd) \\
+        --daughter_outdir "\$(pwd)" \\
         --variant ${sim_data.getBaseName()} \\
         --seed ${lineage_seed} \\
         --lineage_seed ${lineage_seed} \\
@@ -79,7 +79,7 @@ process sim {
         --config $config \\
         --sim_data_path $sim_data \\
         --initial_state_file ${initial_state.getBaseName()} \\
-        --daughter_outdir \$(pwd) \\
+        --daughter_outdir "\$(pwd)" \\
         --variant ${sim_data.getBaseName()} \\
         --seed ${sim_seed} \\
         --lineage_seed ${lineage_seed} \\
diff --git a/runscripts/nextflow/template.nf b/runscripts/nextflow/template.nf
index 662c2b370..825d17d85 100644
--- a/runscripts/nextflow/template.nf
+++ b/runscripts/nextflow/template.nf
@@ -12,7 +12,7 @@ process runParca {
 
     script:
     """
-    PYTHONPATH=${params.projectRoot} python ${params.projectRoot}/runscripts/parca.py --config $config -o \$(pwd)
+    PYTHONPATH=${params.projectRoot} python ${params.projectRoot}/runscripts/parca.py --config "$config" -o "\$(pwd)"
     """
 
     stub:
@@ -37,10 +37,10 @@ process analysisParca {
 
     script:
     """
-    PYTHONPATH=${params.projectRoot} python ${params.projectRoot}/runscripts/analysis.py --config $config \
-        --sim_data_path=$kb/simData.cPickle \
-        --validation_data_path=$kb/validationData.cPickle \
-        -o \$(pwd)/plots \
+    PYTHONPATH=${params.projectRoot} python ${params.projectRoot}/runscripts/analysis.py --config "$config" \
+        --sim_data_path="$kb/simData.cPickle" \
+        --validation_data_path="$kb/validationData.cPickle" \
+        -o "\$(pwd)/plots" \
         -t parca
     """
 
@@ -66,7 +66,7 @@ process createVariants {
     script:
     """
     PYTHONPATH=${params.projectRoot} python ${params.projectRoot}/runscripts/create_variants.py \
-        --config $config --kb $kb -o \$(pwd)
+        --config "$config" --kb "$kb" -o "\$(pwd)"
     """
 
     stub: