diff --git a/.devcontainer/updateContentCommand.sh b/.devcontainer/updateContentCommand.sh index 2bbb246..fa891b8 100644 --- a/.devcontainer/updateContentCommand.sh +++ b/.devcontainer/updateContentCommand.sh @@ -18,9 +18,9 @@ cat < $XDG_CONFIG_HOME/nf-neuro/.env # It is sourced by the shell on startup of every terminals. export PROFILE=docker -export NFCORE_MODULES_GIT_REMOTE=$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)) diff --git a/modules/nf-neuro/tracking/localtracking/main.nf b/modules/nf-neuro/tracking/localtracking/main.nf index cc00b63..3a84e0a 100644 --- a/modules/nf-neuro/tracking/localtracking/main.nf +++ b/modules/nf-neuro/tracking/localtracking/main.nf @@ -1,10 +1,10 @@ process TRACKING_LOCALTRACKING { tag "$meta.id" - label 'process_single' + label 'process_high_memory' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://scil.usherbrooke.ca/containers/scilus_2.0.1.sif': - 'scilus/scilus:2.0.1' }" + 'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif': + 'scilus/scilus:2.0.2' }" input: tuple val(meta), path(wm), path(fodf), path(fa) @@ -39,6 +39,9 @@ process TRACKING_LOCALTRACKING { def compress = task.ext.local_compress_streamlines ? "--compress " + task.ext.local_compress_value : "" def basis = task.ext.basis ? "--sh_basis " + task.ext.basis : "" + def gpu_batch_size = task.ext.gpu_batch_size ? "--batch_size " + task.ext.gpu_batch_size : "" + def enable_gpu = task.ext.enable_gpu ? "--use_gpu $gpu_batch_size" : "" + """ export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1 export OMP_NUM_THREADS=1 @@ -46,35 +49,36 @@ process TRACKING_LOCALTRACKING { if [ "${local_tracking_mask}" == "wm" ]; then scil_volume_math.py convert $wm ${prefix}__local_tracking_mask.nii.gz \ - --data_type uint8 + --data_type uint8 -f elif [ "${local_tracking_mask}" == "fa" ]; then scil_volume_math.py lower_threshold $fa \ $local_fa_tracking_mask_threshold \ ${prefix}__local_tracking_mask.nii.gz \ - --data_type uint8 + --data_type uint8 -f fi if [ "${local_seeding_mask}" == "wm" ]; then scil_volume_math.py convert $wm ${prefix}__local_seeding_mask.nii.gz \ - --data_type uint8 + --data_type uint8 -f elif [ "${local_seeding_mask}" == "fa" ]; then scil_volume_math.py lower_threshold $fa \ $local_fa_seeding_mask_threshold \ ${prefix}__local_seeding_mask.nii.gz \ - --data_type uint8 + --data_type uint8 -f fi - scil_tracking_local.py $fodf ${prefix}__local_seeding_mask.nii.gz ${prefix}__local_tracking_mask.nii.gz tmp.trk\ + scil_tracking_local.py $fodf ${prefix}__local_seeding_mask.nii.gz \ + ${prefix}__local_tracking_mask.nii.gz tmp.trk $enable_gpu\ $local_algo $local_seeding $local_nbr_seeds\ $local_random_seed $local_step $local_theta\ $local_sfthres $local_min_len\ - $local_max_len $compress $basis + $local_max_len $compress $basis -f scil_tractogram_remove_invalid.py tmp.trk\ ${prefix}__local_tracking.trk\ - --remove_single_point + --remove_single_point -f cat <<-TRACKING_INFO > ${prefix}__local_tracking_config.json {"algorithm": "${task.ext.local_algo}", @@ -97,7 +101,7 @@ process TRACKING_LOCALTRACKING { cat <<-END_VERSIONS > versions.yml "${task.process}": - scilpy: 2.0.1 + scilpy: 2.0.2 END_VERSIONS """ @@ -115,7 +119,7 @@ process TRACKING_LOCALTRACKING { cat <<-END_VERSIONS > versions.yml "${task.process}": - scilpy: 2.0.1 + scilpy: 2.0.2 END_VERSIONS """ } diff --git a/modules/nf-neuro/tracking/localtracking/tests/main.nf.test.snap b/modules/nf-neuro/tracking/localtracking/tests/main.nf.test.snap index 3cab094..85d15ec 100644 --- a/modules/nf-neuro/tracking/localtracking/tests/main.nf.test.snap +++ b/modules/nf-neuro/tracking/localtracking/tests/main.nf.test.snap @@ -30,14 +30,14 @@ ] ], [ - "versions.yml:md5,097efc37ca86414ed8d4836991b634b7" + "versions.yml:md5,0088e7190e395324acbb8fce5c474750" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-08T23:46:42.749206" + "timestamp": "2024-10-24T19:38:16.835402429" }, "tracking - localtracking - fa": { "content": [ @@ -70,13 +70,13 @@ ] ], [ - "versions.yml:md5,097efc37ca86414ed8d4836991b634b7" + "versions.yml:md5,0088e7190e395324acbb8fce5c474750" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-08T23:46:28.766414" + "timestamp": "2024-10-24T19:37:54.047881093" } } \ No newline at end of file diff --git a/modules/nf-neuro/tracking/pfttracking/main.nf b/modules/nf-neuro/tracking/pfttracking/main.nf index 47ce697..4aba764 100644 --- a/modules/nf-neuro/tracking/pfttracking/main.nf +++ b/modules/nf-neuro/tracking/pfttracking/main.nf @@ -1,11 +1,11 @@ process TRACKING_PFTTRACKING { tag "$meta.id" - label 'process_single' + label 'process_high_memory' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://scil.usherbrooke.ca/containers/scilus_2.0.1.sif': - 'scilus/scilus:2.0.1' }" + 'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif': + 'scilus/scilus:2.0.2' }" input: tuple val(meta), path(wm), path(gm), path(csf), path(fodf), path(fa) @@ -56,17 +56,17 @@ process TRACKING_PFTTRACKING { if [ "${pft_seeding_mask}" == "wm" ]; then scil_volume_math.py convert $wm ${prefix}__mask_wm.nii.gz \ - --data_type uint8 + --data_type uint8 -f scil_volume_math.py union ${prefix}__mask_wm.nii.gz \ ${prefix}__interface.nii.gz ${prefix}__pft_seeding_mask.nii.gz\ - --data_type uint8 + --data_type uint8 -f elif [ "${pft_seeding_mask}" == "interface" ]; then cp ${prefix}__interface.nii.gz ${prefix}__pft_seeding_mask.nii.gz elif [ "${pft_seeding_mask}" == "fa" ]; then mrcalc $fa $pft_fa_threshold -ge ${prefix}__pft_seeding_mask.nii.gz\ - -datatype uint8 + -datatype uint8 -force fi scil_tracking_pft.py $fodf ${prefix}__pft_seeding_mask.nii.gz \ @@ -74,10 +74,10 @@ process TRACKING_PFTTRACKING { $pft_algo $pft_seeding_type $pft_nbr_seeds \ $pft_random_seed $pft_step $pft_theta\ $pft_sfthres $pft_sfthres_init $pft_min_len $pft_max_len\ - $pft_particles $pft_back $pft_front $compress $basis + $pft_particles $pft_back $pft_front $compress $basis -f scil_tractogram_remove_invalid.py tmp.trk ${prefix}__pft_tracking.trk\ - --remove_single_point + --remove_single_point -f cat <<-TRACKING_INFO > ${prefix}__pft_tracking_config.json {"algorithm": "${task.ext.pft_algo}", @@ -101,7 +101,7 @@ process TRACKING_PFTTRACKING { cat <<-END_VERSIONS > versions.yml "${task.process}": - scilpy: 2.0.1 + scilpy: 2.0.2 mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p') END_VERSIONS """ @@ -124,7 +124,7 @@ process TRACKING_PFTTRACKING { cat <<-END_VERSIONS > versions.yml "${task.process}": - scilpy: 2.0.1 + scilpy: 2.0.2 mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p') END_VERSIONS """ diff --git a/modules/nf-neuro/tracking/pfttracking/tests/main.nf.test.snap b/modules/nf-neuro/tracking/pfttracking/tests/main.nf.test.snap index 92b7ac5..290bbb8 100644 --- a/modules/nf-neuro/tracking/pfttracking/tests/main.nf.test.snap +++ b/modules/nf-neuro/tracking/pfttracking/tests/main.nf.test.snap @@ -39,14 +39,14 @@ ] ], [ - "versions.yml:md5,6fa5c5e21149198626b41120de3947c3" + "versions.yml:md5,2ae3399d07ef00610deae7988357dd55" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-08T23:44:48.372791" + "timestamp": "2024-10-24T19:53:53.332859167" }, "tracking - pfttracking - interface": { "content": [ @@ -79,7 +79,7 @@ ] ], [ - "versions.yml:md5,6fa5c5e21149198626b41120de3947c3" + "versions.yml:md5,2ae3399d07ef00610deae7988357dd55" ], [ [ @@ -92,10 +92,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-08T23:45:02.333851" + "timestamp": "2024-10-24T19:54:04.257171663" }, "tracking - pfttracking - wm": { "content": [ @@ -137,13 +137,13 @@ ] ], [ - "versions.yml:md5,6fa5c5e21149198626b41120de3947c3" + "versions.yml:md5,2ae3399d07ef00610deae7988357dd55" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-08T23:44:33.456248" + "timestamp": "2024-10-24T19:53:38.784232647" } } \ No newline at end of file