[FIX] formatted samplesheets + fix ci action + configs

.github/workflows/ci.yml

@@ -74,4 +74,4 @@ jobs:
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
+          nf-test test ${GITHUB_WORKSPACE} --profile ${{ matrix.profile }}

.nf-core.yml

@@ -9,8 +9,8 @@ lint:
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
     - conf/igenomes.config
-    - assets/FS_BN_GL_SF_utils/**
-    - assets/templates/**
+    - assets/FS_BN_GL_SF_utils/**/*
+    - assets/templates/**/*
   files_unchanged:
     - CODE_OF_CONDUCT.md
     - assets/nf-core-pediatric_logo_light.png

nextflow.config

@@ -224,7 +224,7 @@ params {
     help_full                               = false
     show_hidden                             = false
     version                                 = false
-    pipelines_testdata_base_path            = "${projectDir}/assets/data/"
+    pipelines_testdata_base_path            = "${projectDir}/tests/data/"
 
     // Config options
     config_profile_name                     = null

nextflow_schema.json

@@ -1257,7 +1257,6 @@
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
                     "description": "Base URL or local path to location of pipeline test dataset files",
-                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                     "hidden": true
                 }
             }

tests/data/samplesheet_testconn.csv

@@ -1,2 +1,2 @@
-subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
-sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/labels.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/tracking.trk,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/output1Warp.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/metrics/
+subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
+sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/labels.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/tracking.trk,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/output1Warp.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/metrics/,

tests/data/samplesheet_testconn_nometrics.csv

@@ -1,2 +1,2 @@
-subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
-sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/labels.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/tracking.trk,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/output1Warp.nii.gz,
+subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
+sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/labels.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/tracking.trk,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/output1Warp.nii.gz,,

tests/data/samplesheet_testtracking.csv

@@ -1,2 +1,2 @@
-subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
-sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,,,,,,,
+subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
+sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,,,,,,,,

tests/data/samplesheet_testtracking_infant.csv

@@ -1,2 +1,2 @@
-subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
-sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,,
+subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
+sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,,,

tests/data/samplesheet_testtracking_infant_norev.csv

@@ -1,2 +1,2 @@
-subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
-sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,,
+subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
+sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,,,

tests/data/samplesheet_testtracking_infant_not2.csv

@@ -1,2 +1,2 @@
-subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
-sub-test,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,,
+subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
+sub-test,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,,,

tests/data/samplesheet_testtracking_infant_nowmmask.csv

@@ -1,2 +1,2 @@
-subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
-sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,,,,,,,
+subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
+sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,,,,,,,,

tests/data/samplesheet_testtracking_nodwi.csv

@@ -1,2 +1,2 @@
-subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
-sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,,,,,,,
+subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
+sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,,,,,,,,

tests/data/samplesheet_testtracking_norev.csv

@@ -1,2 +1,2 @@
-subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
-sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,,,,,,,,
+subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
+sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,,,,,,,,,