add protocol to sif images

scilus · Jan 9, 2024 · 2869fac · 2869fac
1 parent 80388fd
commit 2869fac
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Showing 6 changed files with 6 additions and 8 deletions.
diff --git a/docs/MODULE.md b/docs/MODULE.md
@@ -49,7 +49,7 @@ already follow all guidelines. You will find related files in :
 - If the process uses the `scilus` container, use the following replacements,
   else remove the whole section.
 
-  `depot.galaxyproject.org...` &DoubleLongRightArrow; `scil.usherbrooke.ca/containers/scilus_1.6.0.sif`
+  `depot.galaxyproject.org...` &DoubleLongRightArrow; `https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif`
 
   `biocontainers/YOUR-TOOL-HERE` &DoubleLongRightArrow; `scilus/scilus:1.6.0`
 

diff --git a/modules/nf-scil/preproc/gibbs/main.nf b/modules/nf-scil/preproc/gibbs/main.nf
@@ -3,7 +3,7 @@ process PREPROC_GIBBS {
     label 'process_single'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+        'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
         'scilus/scilus:1.6.0' }"
 
     input:

diff --git a/modules/nf-scil/preproc/n4/main.nf b/modules/nf-scil/preproc/n4/main.nf
@@ -3,7 +3,7 @@ process PREPROC_N4 {
     label 'process_single'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+        'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
         'scilus/scilus:1.6.0' }"
 
     input:

diff --git a/modules/nf-scil/testdata/scilpy/main.nf b/modules/nf-scil/testdata/scilpy/main.nf
@@ -4,7 +4,7 @@ process TESTDATA_SCILPY {
     label 'process_single'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+        'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
         'scilus/scilus:1.6.0' }"
 
     input:
@@ -44,4 +44,4 @@ process TESTDATA_SCILPY {
         scilpy: 1.6.0
     END_VERSIONS
     """
-}
+}
diff --git a/modules/nf-scil/tracking/localtracking/main.nf b/modules/nf-scil/tracking/localtracking/main.nf
@@ -3,7 +3,7 @@ process TRACKING_LOCALTRACKING {
     label 'process_single'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+        'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
         'scilus/scilus:1.6.0' }"
 
     input:

diff --git a/tests/modules/nf-scil/denoising/mppca/test.yml b/tests/modules/nf-scil/denoising/mppca/test.yml
@@ -4,8 +4,6 @@
     - denoising/mppca
     - denoising
   files:
-    - path: output/denoising/test__pre_dwi_denoised.nii.gz
-      md5sum: ece4b6fe910ae6502edd52b526609638
     - path: output/denoising/test_dwi_denoised.nii.gz
       md5sum: 0cfa480f702173a047f076bbba9fe25e
     - path: output/denoising/versions.yml