diff --git a/modules/nf-neuro/betcrop/antsbet/main.nf b/modules/nf-neuro/betcrop/antsbet/main.nf index 8fbdf28..dc2867e 100644 --- a/modules/nf-neuro/betcrop/antsbet/main.nf +++ b/modules/nf-neuro/betcrop/antsbet/main.nf @@ -34,12 +34,12 @@ process BETCROP_ANTSBET { -e $template -m $tissues_probabilities ${args.join(' ')} scil_volume_math.py convert bet/BrainExtractionMask.nii.gz \ ${prefix}__t1_bet_mask.nii.gz --data_type uint8 - mrcalc $t1 ${prefix}__t1_bet_mask.nii.gz -mult ${prefix}__t1_bet.nii.gz -nthreads $task.cpus + scil_volume_math.py multiplication $t1 ${prefix}__t1_bet_mask.nii.gz \ + ${prefix}__t1_bet.nii.gz --data_type float32 cat <<-END_VERSIONS > versions.yml "${task.process}": scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) - mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p') ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\+\\).*/\\1/') END_VERSIONS """ @@ -48,13 +48,13 @@ process BETCROP_ANTSBET { def prefix = task.ext.prefix ?: "${meta.id}" """ + touch ${prefix}__t1_bet.nii.gz touch ${prefix}__t1_bet_mask.nii.gz cat <<-END_VERSIONS > versions.yml "${task.process}": scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) - mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p') ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\+\\).*/\\1/') END_VERSIONS @@ -67,6 +67,6 @@ process BETCROP_ANTSBET { antsBrainExtraction.sh scil_volume_math.py -h - mrcalc -h + """ } diff --git a/modules/nf-neuro/betcrop/antsbet/meta.yml b/modules/nf-neuro/betcrop/antsbet/meta.yml index 4ce03b1..e85bfcb 100644 --- a/modules/nf-neuro/betcrop/antsbet/meta.yml +++ b/modules/nf-neuro/betcrop/antsbet/meta.yml @@ -10,9 +10,6 @@ tools: - "scilpy": description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox." homepage: "https://github.com/scilus/scilpy.git" - - "MRtrix3": - description: "Toolbox for image processing, analysis and visualisation of dMRI." - homepage: "https://mrtrix.readthedocs.io/en/latest/" - "ants": description: "Advanced Normalization Tools." homepage: "https://github.com/ANTsX/ANTs" diff --git a/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test b/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test index bd15b35..c42aa6b 100644 --- a/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test +++ b/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test @@ -70,7 +70,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - niftiMD5SUM(process.out.t1.get(0).get(1)), + niftiMD5SUM(process.out.t1.get(0).get(1), 1), niftiMD5SUM(process.out.mask.get(0).get(1)), process.out.versions ).match() } diff --git a/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap b/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap index b76e32d..8777011 100644 --- a/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap +++ b/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap @@ -1,28 +1,28 @@ { "betcrop - antsbet": { "content": [ - "test__t1_bet.nii.gz:md5:header,72167012fa8893d3c3531d5d1245b84a,data,e31b24e1dadf5b067211544fca1f3f01", + "test__t1_bet.nii.gz:md5:header,e7cfbd06624321d70cbd667a77315ba3,data,381da559c1f38a2526f58b741eb0f7fc", "test__t1_bet_mask.nii.gz:md5:header,f7389fe98c9a7e3a87c90b7ca05ea14a,data,1572808125554e50ff73fbe0e28037a9", [ - "versions.yml:md5,9fde1445bc10857db69e440781e58cb7" + "versions.yml:md5,bb378e913d4002d0b644d3277892ae20" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T20:31:09.4739" + "timestamp": "2025-01-15T16:55:54.33351491" }, "betcrop - antsbet - stub-run": { "content": [ [ - "versions.yml:md5,9fde1445bc10857db69e440781e58cb7" + "versions.yml:md5,bb378e913d4002d0b644d3277892ae20" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-12T10:20:29.72452" + "timestamp": "2025-01-14T20:42:47.191136661" } } \ No newline at end of file diff --git a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap index 7f6ebec..a126dee 100644 --- a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap +++ b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap @@ -297,18 +297,18 @@ "test_cropped.nii.gz", "test_t1_cropped.nii.gz", [ - "versions.yml:md5,19aaa24cf046e49a4ad4ce5d507ea8aa", "versions.yml:md5,37229cd5cee6f6788fbc9083d6618c61", "versions.yml:md5,657fbb224f260392e573b8511c4b798d", "versions.yml:md5,b979132991d8f72a3585465533bd5730", "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740", + "versions.yml:md5,da278daafbe3afa8454021e2716dd205", "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.10.0" }, - "timestamp": "2024-12-04T10:38:12.185789" + "timestamp": "2024-12-12T15:50:29.838128539" } } \ No newline at end of file