From 171def89178a1da0bd9753110849b403b0e99ecb Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 17 Nov 2023 08:33:24 -0500
Subject: [PATCH 1/2] chore: remove echo from debugging

---
 modules/local/deeptools.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/local/deeptools.nf b/modules/local/deeptools.nf
index aa2758ed..625b9118 100644
--- a/modules/local/deeptools.nf
+++ b/modules/local/deeptools.nf
@@ -256,7 +256,6 @@ process COMPUTE_MATRIX {
     error "Invalid matrix type: ${mattype}"
   }
   """
-  echo "$mattype" > file.txt
   computeMatrix ${cmd} \\
     -S ${bigwigs.sort({ a, b -> a.baseName <=> b.baseName }).join(' ')} \\
     -R ${bed} \\

From 36052a3478dbf38cc8f5a6520f0102067111b34e Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 17 Nov 2023 10:19:38 -0500
Subject: [PATCH 2/2] fix: don't run chmod_bins_exect() in run function

but do run it after installation in the github action
---
 .github/workflows/build.yml | 1 +
 src/util.py                 | 2 --
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 72e4e77c..20d29e54 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -39,6 +39,7 @@ jobs:
           python -m pip install --upgrade pip setuptools
           mkdir -p tests/bin/
           pip install .[dev,test]
+          python -c 'from champagne.src.util import chmod_bins_exec; chmod_bins_exec()'
       - name: Stub run
         run: |
           cd tests/cli
diff --git a/src/util.py b/src/util.py
index 42b860c8..03c94a15 100644
--- a/src/util.py
+++ b/src/util.py
@@ -153,8 +153,6 @@ def run_nextflow(
 ):
     """Run a Nextflow workflow"""
     nextflow_command = ["nextflow", "run", nextfile_path]
-    # make sure bins are executable for nextflow processes
-    chmod_bins_exec()
 
     hpc = get_hpc()
     if mode == "slurm" and not hpc: