From 87cd586661151b08a0f57992a86fb63db86bfe6e Mon Sep 17 00:00:00 2001 From: arnaudbore Date: Thu, 24 Oct 2024 19:04:52 +0000 Subject: [PATCH 1/2] changes done but no test run yey --- modules/nf-neuro/io/readbids/main.nf | 24 +++++++++---------- modules/nf-neuro/io/readbids/meta.yml | 8 +++---- .../nf-neuro/io/readbids/tests/main.nf.test | 9 +++---- 3 files changed, 20 insertions(+), 21 deletions(-) diff --git a/modules/nf-neuro/io/readbids/main.nf b/modules/nf-neuro/io/readbids/main.nf index 1c2447c..64c7b8d 100644 --- a/modules/nf-neuro/io/readbids/main.nf +++ b/modules/nf-neuro/io/readbids/main.nf @@ -2,13 +2,11 @@ process IO_READBIDS { label 'process_single' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif': - 'scilus/scilus:2.0.0' }" + 'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif': + 'scilus/scilus:2.0.2' }" input: - path(bids_folder) - path(fsfolder) - path(bidsignore) + tuple path(bids_folder), path(fs_folder), path(bids_ignore) output: path("tractoflow_bids_struct.json") , emit: bidsstructure @@ -20,22 +18,22 @@ process IO_READBIDS { script: def args = task.ext.args ?: '' - def fsfolder = task.ext.fs_folder ? "--fs " + task.ext.fs_folder : '' - def bidsignore = task.ext.bidsignore ? "--bids_ignore " + task.ext.bidsignore : '' - def readout = task.ext.readout ? "--readout " + task.ext.readout : "" - def clean_flag = task.ext.clean_bids ? '--clean ' : '' + def fs_folder = fs_folder ? "--fs $fs_folder" : '' + def bids_ignore = bidsignore ? "--bids_ignore $bids_ignore" : '' + def readout = task.ext.readout ? "--readout " + task.ext.readout : '' + def clean_flag = task.ext.clean_bids ? "--clean " : '' """ scil_bids_validate.py $bids_folder tractoflow_bids_struct.json\ $readout \ $clean_flag\ - $fsfolder\ - $bidsignore\ + $fs_folder\ + $bids_ignore\ -v cat <<-END_VERSIONS > versions.yml "${task.process}": - scilpy: 2.0.0 + scilpy: 2.0.2 END_VERSIONS """ @@ -49,7 +47,7 @@ process IO_READBIDS { cat <<-END_VERSIONS > versions.yml "${task.process}": - scilpy: 2.0.0 + scilpy: 2.0.2 END_VERSIONS """ } diff --git a/modules/nf-neuro/io/readbids/meta.yml b/modules/nf-neuro/io/readbids/meta.yml index 7005068..d1296a3 100644 --- a/modules/nf-neuro/io/readbids/meta.yml +++ b/modules/nf-neuro/io/readbids/meta.yml @@ -16,15 +16,15 @@ input: description: Folder containing bids file pattern: "*" - - fsfolder: + - fs_folder: type: directory description: Folder containing fs file pattern: "*" - - bidsignore: + - bids_ignore: type: file - description: bidsignore file - pattern: "*.{bidsignore}" + description: bids_ignore file + pattern: "*.{bids_ignore}" output: - versions: diff --git a/modules/nf-neuro/io/readbids/tests/main.nf.test b/modules/nf-neuro/io/readbids/tests/main.nf.test index 1a5a1cb..61436dd 100644 --- a/modules/nf-neuro/io/readbids/tests/main.nf.test +++ b/modules/nf-neuro/io/readbids/tests/main.nf.test @@ -30,11 +30,12 @@ nextflow_process { process { """ input[0] = LOAD_DATA.out.test_data_directory.map{ - test_data_directory -> - file("\${test_data_directory}/i_bids", checkIfExists: true) + test_data_directory -> [ + file("\${test_data_directory}/i_bids", checkIfExists: true), + [], + [], + ] } - input[1] = [] - input[2] = [] """ } } From 0f69c3c7f49f3751d5ed08b2d776be19dca114f5 Mon Sep 17 00:00:00 2001 From: arnaudbore Date: Thu, 24 Oct 2024 19:44:29 +0000 Subject: [PATCH 2/2] update snap and fix tests --- .devcontainer/updateContentCommand.sh | 4 ++-- modules/nf-neuro/io/readbids/main.nf | 2 +- modules/nf-neuro/io/readbids/tests/main.nf.test.snap | 10 +++++----- 3 files changed, 8 insertions(+), 8 deletions(-) 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/io/readbids/main.nf b/modules/nf-neuro/io/readbids/main.nf index 64c7b8d..dd5c4e2 100644 --- a/modules/nf-neuro/io/readbids/main.nf +++ b/modules/nf-neuro/io/readbids/main.nf @@ -19,7 +19,7 @@ process IO_READBIDS { script: def args = task.ext.args ?: '' def fs_folder = fs_folder ? "--fs $fs_folder" : '' - def bids_ignore = bidsignore ? "--bids_ignore $bids_ignore" : '' + def bids_ignore = bids_ignore ? "--bids_ignore $bids_ignore" : '' def readout = task.ext.readout ? "--readout " + task.ext.readout : '' def clean_flag = task.ext.clean_bids ? "--clean " : '' diff --git a/modules/nf-neuro/io/readbids/tests/main.nf.test.snap b/modules/nf-neuro/io/readbids/tests/main.nf.test.snap index 69f77a9..3edae7a 100644 --- a/modules/nf-neuro/io/readbids/tests/main.nf.test.snap +++ b/modules/nf-neuro/io/readbids/tests/main.nf.test.snap @@ -6,20 +6,20 @@ "tractoflow_bids_struct.json:md5,58e0494c51d30eb3494f7c9198986bb9" ], "1": [ - "versions.yml:md5,0af9864a1818468702fa7d6ac7985e29" + "versions.yml:md5,53cf301d7d6076acbc0691d3e7e52437" ], "bidsstructure": [ "tractoflow_bids_struct.json:md5,58e0494c51d30eb3494f7c9198986bb9" ], "versions": [ - "versions.yml:md5,0af9864a1818468702fa7d6ac7985e29" + "versions.yml:md5,53cf301d7d6076acbc0691d3e7e52437" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-29T20:34:58.293363" + "timestamp": "2024-10-24T19:43:56.536400136" } } \ No newline at end of file