Replace the bash shell path according to this: nextflow-io/nextflow#2341

.github/scripts/install_conda.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -eo pipefail
 
 echo Install Conda .. >> artifacts/test_artifact.log
@@ -8,7 +8,7 @@ sudo apt-get update --fix-missing && sudo apt-get install -y wget bzip2 ca-certi
     libglib2.0-0 libxext6 libsm6 libxrender1 \
     git mercurial subversion
 wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
-    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
+    /usr/bin/env bash ~/miniconda.sh -b -p /opt/conda && \
     rm ~/miniconda.sh && \
     ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
     echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \

.github/scripts/install_singularity.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -eo pipefail
 
 echo Install Singularity dependencies.. >> artifacts/test_artifact.log

.github/scripts/test_PR_against_release.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -eo pipefail
 export PATH=/opt/conda/bin:$PATH
 

.github/scripts/test_bed_ref_input.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -eo pipefail
 export PATH=/opt/conda/bin:$PATH
 

.github/scripts/test_conda_cache.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -eo pipefail
 export PATH=/opt/conda/bin:$PATH
 

.github/scripts/test_cram_input.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -eo pipefail
 export PATH=/opt/conda/bin:$PATH
 

.github/scripts/test_cram_output.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -eo pipefail
 export PATH=/opt/conda/bin:$PATH
 

.github/scripts/test_nanopore_pipelines.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -eo pipefail
 export PATH=/opt/conda/bin:$PATH
 

.github/scripts/test_sanger_profile.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -eo pipefail
 export PATH=/opt/conda/bin:$PATH
 

.github/scripts/test_typing.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -eo pipefail
 export PATH=/opt/conda/bin:$PATH
 

nextflow.config

@@ -508,7 +508,7 @@ profiles {
 includeConfig 'conf/coguk.config'
 
 // Capture exit codes from upstream processes when piping
-process.shell = ['/bin/bash', '-euo', 'pipefail']
+process.shell = ['/usr/bin/env bash', '-euo', 'pipefail']
 
 manifest {
     author = 'Matt Bull'

tests/GPAS_tests.bash

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 rm -rf /work/runs/*_test /work/output/*_test
 

tests/GPAS_tests_just_summaries.bash

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 #source ~/env/bin/activate
 
 # ont_artic_test

tests/GPAS_tests_short.bash

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 
 echo \

tests/update_expected.bash

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 tests="ont_artic
 ont_viridian

tests/update_expected_short.bash

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 tests="ont_artic_short
 ont_viridian_short