[ENH] io module

.devcontainer/updateContentCommand.sh

@@ -18,9 +18,9 @@ cat <<EOF > $XDG_CONFIG_HOME/nf-neuro/.env
 # It is sourced by the shell on startup of every terminals.
 
 export PROFILE=docker
-export NFCORE_MODULES_GIT_REMOTE=$GIT_REMOTE
+export NFCORE_MODULES_GIT_REMOTE="$GIT_REMOTE"
 export NFCORE_MODULES_BRANCH=$CURRENT_BRANCH
-export NFCORE_SUBWORKFLOWS_GIT_REMOTE=$GIT_REMOTE
+export NFCORE_SUBWORKFLOWS_GIT_REMOTE="$GIT_REMOTE"
 export NFCORE_SUBWORKFLOWS_BRANCH=$CURRENT_BRANCH
 
 export DEVCONTAINER_RAM_LIMIT_GB=$((maxmem / 1024 / 1024))

modules/nf-neuro/io/readbids/main.nf

@@ -2,13 +2,11 @@ process IO_READBIDS {
     label 'process_single'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif':
-        'scilus/scilus:2.0.0' }"
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
 
     input:
-        path(bids_folder)
-        path(fsfolder)
-        path(bidsignore)
+        tuple path(bids_folder), path(fs_folder), path(bids_ignore)
 
     output:
         path("tractoflow_bids_struct.json")             , emit: bidsstructure
@@ -20,22 +18,22 @@ process IO_READBIDS {
 
     script:
     def args = task.ext.args ?: ''
-    def fsfolder = task.ext.fs_folder ? "--fs " + task.ext.fs_folder : ''
-    def bidsignore = task.ext.bidsignore ? "--bids_ignore " + task.ext.bidsignore : ''
-    def readout = task.ext.readout ? "--readout " + task.ext.readout : ""
-    def clean_flag = task.ext.clean_bids ? '--clean ' : ''
+    def fs_folder = fs_folder ? "--fs $fs_folder" : ''
+    def bids_ignore = bids_ignore ? "--bids_ignore $bids_ignore" : ''
+    def readout = task.ext.readout ? "--readout " + task.ext.readout : ''
+    def clean_flag = task.ext.clean_bids ? "--clean " : ''
 
     """
     scil_bids_validate.py $bids_folder tractoflow_bids_struct.json\
         $readout \
         $clean_flag\
-        $fsfolder\
-        $bidsignore\
+        $fs_folder\
+        $bids_ignore\
         -v
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.0
+        scilpy: 2.0.2
     END_VERSIONS
     """
 
@@ -49,7 +47,7 @@ process IO_READBIDS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.0
+        scilpy: 2.0.2
     END_VERSIONS
     """
 }

modules/nf-neuro/io/readbids/meta.yml

@@ -16,15 +16,15 @@ input:
       description: Folder containing bids file
       pattern: "*"
 
-  - fsfolder:
+  - fs_folder:
       type: directory
       description: Folder containing fs file
       pattern: "*"
 
-  - bidsignore:
+  - bids_ignore:
       type: file
-      description: bidsignore file
-      pattern: "*.{bidsignore}"
+      description: bids_ignore file
+      pattern: "*.{bids_ignore}"
 
 output:
   - versions:

modules/nf-neuro/io/readbids/tests/main.nf.test

@@ -30,11 +30,12 @@ nextflow_process {
             process {
                 """
                 input[0] = LOAD_DATA.out.test_data_directory.map{
-                    test_data_directory ->
-                        file("\${test_data_directory}/i_bids", checkIfExists: true)
+                    test_data_directory -> [
+                        file("\${test_data_directory}/i_bids", checkIfExists: true),
+                        [],
+                        [],
+                    ]
                 }
-                input[1] = []
-                input[2] = []
                 """
             }
         }

modules/nf-neuro/io/readbids/tests/main.nf.test.snap

@@ -6,20 +6,20 @@
                     "tractoflow_bids_struct.json:md5,58e0494c51d30eb3494f7c9198986bb9"
                 ],
                 "1": [
-                    "versions.yml:md5,0af9864a1818468702fa7d6ac7985e29"
+                    "versions.yml:md5,53cf301d7d6076acbc0691d3e7e52437"
                 ],
                 "bidsstructure": [
                     "tractoflow_bids_struct.json:md5,58e0494c51d30eb3494f7c9198986bb9"
                 ],
                 "versions": [
-                    "versions.yml:md5,0af9864a1818468702fa7d6ac7985e29"
+                    "versions.yml:md5,53cf301d7d6076acbc0691d3e7e52437"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-29T20:34:58.293363"
+        "timestamp": "2024-10-24T19:43:56.536400136"
     }
 }