Deeparg singularity container fix 2 (#1406)

* fix: remove left-over unnecessary code

* Switch to more portable solution for singularity container issue by using bind paths

* Fix input collision of dummy files

* Repalce dummy with which bash

* Remove dummy usage from tests

* Apply suggestions from code review

* Fix singularity typo

modules/deeparg/downloaddata/main.nf

@@ -8,10 +8,10 @@ process DEEPARG_DOWNLOADDATA {
         'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' :
         'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
     /*
-    We have to force singularity to run with --fakeroot to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
+    We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
-    This flag may not be available on all systems and may be considered a security problem. so please document and /or warn for this in your pipeline!
+    Original report: https://github.com/nf-core/funcscan/issues/23
     */
-    containerOptions { "${workflow.containerEngine}" == 'singularity' ? '--fakeroot' : '' }
+    containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' }
 
 
     input:

modules/deeparg/downloaddata/meta.yml

@@ -17,7 +17,7 @@ tools:
       licence: ["MIT"]
 
 input:
-  - none: There is no input. This module downloads a pre-built database for use with deepARG.
+  - none: No input required for download module.
 
 output:
   - versions:

modules/deeparg/predict/main.nf

@@ -6,13 +6,13 @@ process DEEPARG_PREDICT {
 
     conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity//deeparg:1.0.2--pyhdfd78af_1' :
+        'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' :
         'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
     /*
-    We have to force singularity to run with --fakeroot to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
+    We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
-    This flag may not be available on all systems and may be considered a security problem. so please document and /or warn for this in your pipeline!
+        Original report: https://github.com/nf-core/funcscan/issues/23
     */
-    containerOptions { "${workflow.containerEngine}" == 'singularity' ? '--fakeroot' : '' }
+    containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' }
 
     input:
     tuple val(meta), path(fasta), val(model)

tests/modules/deeparg/downloaddata/main.nf

@@ -5,5 +5,5 @@ nextflow.enable.dsl = 2
 include { DEEPARG_DOWNLOADDATA } from '../../../../modules/deeparg/downloaddata/main.nf'
 
 workflow test_deeparg_downloaddata {
-    DEEPARG_DOWNLOADDATA ()
+    DEEPARG_DOWNLOADDATA ( )
 }

tests/modules/deeparg/predict/main.nf

@@ -13,7 +13,7 @@ workflow test_deeparg_predict {
         'LS'
     ]
 
-    DEEPARG_DOWNLOADDATA()
+    DEEPARG_DOWNLOADDATA( )
     DEEPARG_PREDICT ( input, DEEPARG_DOWNLOADDATA.out.db )
 
 }