Manage synth conditionnality through params instead of input

scilus · Aug 31, 2024 · 0a16b4d · 0a16b4d
1 parent fdb32e5
commit 0a16b4d
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Showing 4 changed files with 13 additions and 12 deletions.
diff --git a/subworkflows/nf-scil/preproc_t1/main.nf b/subworkflows/nf-scil/preproc_t1/main.nf
@@ -7,6 +7,8 @@ include { BETCROP_SYNTHBET} from '../../../modules/nf-scil/betcrop/synthbet/main
 include { BETCROP_CROPVOLUME as BETCROP_CROPVOLUME_T1 } from '../../../modules/nf-scil/betcrop/cropvolume/main'
 include { BETCROP_CROPVOLUME as BETCROP_CROPVOLUME_MASK } from '../../../modules/nf-scil/betcrop/cropvolume/main'
 
+params.run_synth = params.run_synth ?: false
+
 workflow PREPROC_T1 {
 
     take:
@@ -18,8 +20,6 @@ workflow PREPROC_T1 {
         ch_ref_resample    // channel: [ val(meta), [ ref ] ]             , optional
         ch_weights         // channel: [ val(meta), [ weights ] ]         , optional
 
-        val_synth(false)   // value: (default: false)                     , optional
-
     main:
 
         ch_versions = Channel.empty()
@@ -40,7 +40,7 @@ workflow PREPROC_T1 {
         ch_versions = ch_versions.mix(IMAGE_RESAMPLE.out.versions.first())
 
         // ** Brain extraction ** //
-        if ( val_synth ) {
+        if ( params.run_synth ) {
             ch_bet = IMAGE_RESAMPLE.out.image.join(ch_weights)
             BETCROP_SYNTHBET ( ch_bet )
             ch_versions = ch_versions.mix(BETCROP_SYNTHBET.out.versions.first())

diff --git a/subworkflows/nf-scil/preproc_t1/tests/main.nf.test b/subworkflows/nf-scil/preproc_t1/tests/main.nf.test
@@ -75,7 +75,6 @@ nextflow_workflow {
                         [ id:'test', single_end:false ],
                         []
                     ]}
-                input[7] = false
                 """
             }
         }
@@ -135,7 +134,6 @@ nextflow_workflow {
                         [ id:'test', single_end:false ],
                         []
                     ]}
-                input[7] = false
                 """
             }
         }
@@ -195,7 +193,6 @@ test("preproc_t1_synth") {
                         [ id:'test', single_end:false ],
                         []
                     ]}
-                input[7] = true
                 """
             }
         }

diff --git a/subworkflows/nf-scil/preproc_t1/tests/main.nf.test.snap b/subworkflows/nf-scil/preproc_t1/tests/main.nf.test.snap
@@ -166,9 +166,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0-rc1",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-30T20:24:23.951944"
+        "timestamp": "2024-08-27T16:07:20.834954"
     },
     "preproc_t1_synth": {
         "content": [
@@ -337,9 +337,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0-rc1",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-30T19:21:50.686836"
+        "timestamp": "2024-08-27T16:12:58.594953"
     },
     "preproc_t1_classic": {
         "content": [
@@ -508,8 +508,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0-rc1",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-30T20:05:33.018053"
+        "timestamp": "2024-08-27T15:48:27.520928"
     }
 }
diff --git a/subworkflows/nf-scil/preproc_t1/tests/nextflow_synth.config b/subworkflows/nf-scil/preproc_t1/tests/nextflow_synth.config
@@ -12,3 +12,7 @@ process {
         memory = 8.GB
     }
 }
+
+params {
+    run_synth = true
+}