From a318861a275db5cf0b36a79c408b0fd43d5b0e46 Mon Sep 17 00:00:00 2001 From: anroy1 Date: Wed, 4 Sep 2024 17:44:01 +0000 Subject: [PATCH] Delete to fsl tests as not implemented --- .../registration/convert/tests/main.nf.test | 104 ------------------ .../convert/tests/nextflow_antsfsl.config | 7 -- .../convert/tests/nextflow_fsfsl.config | 9 -- 3 files changed, 120 deletions(-) delete mode 100644 modules/nf-scil/registration/convert/tests/nextflow_antsfsl.config delete mode 100644 modules/nf-scil/registration/convert/tests/nextflow_fsfsl.config diff --git a/modules/nf-scil/registration/convert/tests/main.nf.test b/modules/nf-scil/registration/convert/tests/main.nf.test index b8039172..340238c6 100644 --- a/modules/nf-scil/registration/convert/tests/main.nf.test +++ b/modules/nf-scil/registration/convert/tests/main.nf.test @@ -121,60 +121,6 @@ nextflow_process { } } - // FSL output not fully implemented in mri_warp_convert - - // test("registration - convert - fsfsl") { - - // config "./nextflow_fsfsl.config" - - // when { - // process { - // """ - // input[0] = LOAD_DATA.out.test_data_directory.map{ - // test_data_directory -> [ - // ch_split_test_data = LOAD_DATA.out.test_data_directory - // .branch{ - // freesurfer: it.simpleName == "freesurfer" - // reslice: it.simpleName == "freesurfer_reslice" - // transforms: it.simpleName == "freesurfer_transforms" - // } - // ch_transforms = ch_split_test_data.transforms.map{ - // test_data_directory -> [ - // [ id:'test' ], - // file("\${test_data_directory}/fs_deform.nii.gz"), - // file("\${test_data_directory}/fs_affine.lta") - // ] - // } - // ch_reslice = ch_split_test_data.reslice.map{ - // test_data_directory -> [ - // [ id:'test' ], - // file("\${test_data_directory}/t1_reslice.nii.gz"), - // file("\${test_data_directory}/fa_reslice.nii.gz") - // ] - // } - // ch_freesurfer = ch_split_test_data.freesurfer.map{ - // test_data_directory -> [ - // [ id:'test' ], - // file("\${test_data_directory}/license.txt") - // ] - // } - // input[0] = ch_transforms - // .join(ch_reslice) - // .join(ch_freesurfer) - // ] - // } - // """ - // } - // } - - // then { - // assertAll( - // { assert process.success }, - // { assert snapshot(process.out).match() } - // ) - // } - // } - test("registration - convert - fslfs") { config "./nextflow_fslfs.config" @@ -318,54 +264,4 @@ nextflow_process { ) } } - - // FSL output not fully implemented in mri_warp_convert - - // test("registration - convert - antsfsl") { - - // config "./nextflow_antsfsl.config" - - // when { - // process { - // """ - // ch_split_test_data = LOAD_DATA.out.test_data_directory - // .branch{ - // freesurfer: it.simpleName == "freesurfer" - // reslice: it.simpleName == "freesurfer_reslice" - // transforms: it.simpleName == "freesurfer_transforms" - // } - // ch_transforms = ch_split_test_data.transforms.map{ - // test_data_directory -> [ - // [ id:'test' ], - // file("\${test_data_directory}/ants_deform.nii.gz"), - // file("\${test_data_directory}/ants_affine.lta") - // ] - // } - // ch_reslice = ch_split_test_data.reslice.map{ - // test_data_directory -> [ - // [ id:'test' ], - // file("\${test_data_directory}/t1_reslice.nii.gz"), - // file("\${test_data_directory}/fa_reslice.nii.gz") - // ] - // } - // ch_freesurfer = ch_split_test_data.freesurfer.map{ - // test_data_directory -> [ - // [ id:'test' ], - // file("\${test_data_directory}/license.txt") - // ] - // } - // input[0] = ch_transforms - // .join(ch_reslice) - // .join(ch_freesurfer) - // """ - // } - // } - - // then { - // assertAll( - // { assert process.success }, - // { assert snapshot(process.out).match() } - // ) - // } - // } } diff --git a/modules/nf-scil/registration/convert/tests/nextflow_antsfsl.config b/modules/nf-scil/registration/convert/tests/nextflow_antsfsl.config deleted file mode 100644 index 3575946a..00000000 --- a/modules/nf-scil/registration/convert/tests/nextflow_antsfsl.config +++ /dev/null @@ -1,7 +0,0 @@ -process { - withName: "REGISTRATION_CONVERT" { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - ext.invert = "true" - ext.downsample = "true" - } -} diff --git a/modules/nf-scil/registration/convert/tests/nextflow_fsfsl.config b/modules/nf-scil/registration/convert/tests/nextflow_fsfsl.config deleted file mode 100644 index 6629dea2..00000000 --- a/modules/nf-scil/registration/convert/tests/nextflow_fsfsl.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - withName: "REGISTRATION_CONVERT" { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - ext.in_format_init = "lta" - ext.out_format_init = "fsl" - ext.in_format_deform = "ras" - ext.out_format_deform = "fsl" - } -}