diff --git a/laxy_downloader/README.md b/laxy_downloader/README.md
index a196a0b..0bdaa19 100644
--- a/laxy_downloader/README.md
+++ b/laxy_downloader/README.md
@@ -6,7 +6,7 @@ Intended to be run by the job script on a compute node.
 ### Install
 
 ```bash
-pip install -e git+https://github.com/MonashBioinformaticsPlatform/laxy/laxy_downloader@master#egg=laxy_downloader
+pip install -e "laxy_downloader @ git+https://github.com/MonashBioinformaticsPlatform/laxy@master#egg=laxy_downloader&subdirectory=laxy_downloader"
 ```
 
 ### Usage
diff --git a/laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/3.12.0/scripts/run_job.sh b/laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/3.12.0/scripts/run_job.sh
index a59c35f..b3d321c 100755
--- a/laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/3.12.0/scripts/run_job.sh
+++ b/laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/3.12.0/scripts/run_job.sh
@@ -38,9 +38,9 @@ export PIPELINES_CACHE_PATH="${JOB_PATH}/../../cache/pipelines"
 export SINGULARITY_TMPDIR="${TMPDIR}"
 export AUTH_HEADER_FILE="${JOB_PATH}/.private_request_headers"
 export IGNORE_SELF_SIGNED_CERTIFICATE="{{ IGNORE_SELF_SIGNED_CERTIFICATE }}"
-export LAXYDL_BRANCH=master
+export LAXYDL_BRANCH=${LAXYDL_BRANCH:-master}
 export LAXYDL_USE_ARIA2C=${LAXYDL_USE_ARIA2C:-yes}
-export LAXYDL_PARALLEL_DOWNLOADS=8
+export LAXYDL_PARALLEL_DOWNLOADS=${LAXYDL_PARALLEL_DOWNLOADS:-8}
 
 # These are applied via chmod to all files and directories in the run, upon completion
 export JOB_FILE_PERMS='ug+rw-s,o='
diff --git a/laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/default/input/scripts/env.sh b/laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/default/input/scripts/env.sh
index aa9a0dd..cc4262a 100644
--- a/laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/default/input/scripts/env.sh
+++ b/laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/default/input/scripts/env.sh
@@ -23,9 +23,9 @@ export SINGULARITY_CACHEDIR="${JOB_PATH}/../../cache/singularity"
 export SINGULARITY_TMPDIR="${TMP}"
 export AUTH_HEADER_FILE="${JOB_PATH}/.private_request_headers"
 export IGNORE_SELF_SIGNED_CERTIFICATE="{{ IGNORE_SELF_SIGNED_CERTIFICATE }}"
-export LAXYDL_BRANCH=master
+export LAXYDL_BRANCH=${LAXYDL_BRANCH:-master}
 export LAXYDL_USE_ARIA2C=${LAXYDL_USE_ARIA2C:-yes}
-export LAXYDL_PARALLEL_DOWNLOADS=8
+export LAXYDL_PARALLEL_DOWNLOADS=${LAXYDL_PARALLEL_DOWNLOADS:-8}
 
 # These are applied via chmod to all files and directories in the run, upon completion
 export JOB_FILE_PERMS='ug+rw-s,o='
diff --git a/laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/default/input/scripts/run_job.sh b/laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/default/input/scripts/run_job.sh
index 01282e2..76457d5 100755
--- a/laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/default/input/scripts/run_job.sh
+++ b/laxy_pipeline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/default/input/scripts/run_job.sh
@@ -38,9 +38,9 @@ export PIPELINES_CACHE_PATH="${JOB_PATH}/../../cache/pipelines"
 export SINGULARITY_TMPDIR="${TMPDIR}"
 export AUTH_HEADER_FILE="${JOB_PATH}/.private_request_headers"
 export IGNORE_SELF_SIGNED_CERTIFICATE="{{ IGNORE_SELF_SIGNED_CERTIFICATE }}"
-export LAXYDL_BRANCH=master
+export LAXYDL_BRANCH=${LAXYDL_BRANCH:-master}
 export LAXYDL_USE_ARIA2C=${LAXYDL_USE_ARIA2C:-yes}
-export LAXYDL_PARALLEL_DOWNLOADS=8
+export LAXYDL_PARALLEL_DOWNLOADS=${LAXYDL_PARALLEL_DOWNLOADS:-8}
 
 # These are applied via chmod to all files and directories in the run, upon completion
 export JOB_FILE_PERMS='ug+rw-s,o='