From 3fab00364b4f6389587a0325e865757f6b4c20b4 Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Wed, 12 Feb 2025 21:25:09 +0000 Subject: [PATCH] bump: Updated all modules. --- modules.json | 14 +-- modules/nf-core/cellpose/main.nf | 8 +- modules/nf-core/cellpose/meta.yml | 68 ++++++++------ modules/nf-core/cellpose/tests/main.nf.test | 4 +- modules/nf-core/deepcell/mesmer/main.nf | 2 +- modules/nf-core/deepcell/mesmer/meta.yml | 62 +++++++------ .../deepcell/mesmer/tests/main.nf.test | 2 +- .../nf-core/ilastik/multicut/environment.yml | 5 - modules/nf-core/ilastik/multicut/meta.yml | 92 ++++++++++--------- .../pixelclassification/environment.yml | 5 - .../ilastik/pixelclassification/meta.yml | 70 +++++++------- .../mindagap/duplicatefinder/environment.yml | 6 +- .../nf-core/mindagap/duplicatefinder/meta.yml | 52 ++++++----- .../nf-core/mindagap/mindagap/environment.yml | 2 + modules/nf-core/multiqc/environment.yml | 2 + .../nf-core/multiqc/tests/main.nf.test.snap | 2 +- 16 files changed, 211 insertions(+), 185 deletions(-) delete mode 100644 modules/nf-core/ilastik/multicut/environment.yml delete mode 100644 modules/nf-core/ilastik/pixelclassification/environment.yml diff --git a/modules.json b/modules.json index 12a36c1..a313ac8 100644 --- a/modules.json +++ b/modules.json @@ -7,37 +7,37 @@ "nf-core": { "cellpose": { "branch": "master", - "git_sha": "7c1543a730197e2f0b8ca5141f851c4a2b08bed6", + "git_sha": "5bca12d66725b17a486edc24d1d2381d4170da25", "installed_by": ["modules"] }, "deepcell/mesmer": { "branch": "master", - "git_sha": "298406de7fb599b3a7acfed1dddb606ec182d4b6", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "ilastik/multicut": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "a4d916a39231897a49c903089a548704c09b8ef3", "installed_by": ["modules"] }, "ilastik/pixelclassification": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "a4d916a39231897a49c903089a548704c09b8ef3", "installed_by": ["modules"] }, "mindagap/duplicatefinder": { "branch": "master", - "git_sha": "cdc42519bf7d6d2cac9b5f14cb56e0060477c69c", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "mindagap/mindagap": { "branch": "master", - "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] } } diff --git a/modules/nf-core/cellpose/main.nf b/modules/nf-core/cellpose/main.nf index f100904..967ff34 100644 --- a/modules/nf-core/cellpose/main.nf +++ b/modules/nf-core/cellpose/main.nf @@ -24,8 +24,9 @@ process CELLPOSE { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def model_command = model ? "--pretrained_model $model" : "" - def VERSION = '3.0.1' """ + export OMP_NUM_THREADS=${task.cpus} + export MKL_NUM_THREADS=${task.cpus} cellpose \\ --image_path $image \\ --save_tif \\ @@ -34,7 +35,7 @@ process CELLPOSE { cat <<-END_VERSIONS > versions.yml "${task.process}": - cellpose: $VERSION + cellpose: \$(cellpose --version | awk 'NR==2 {print \$3}') END_VERSIONS """ stub: @@ -43,7 +44,6 @@ process CELLPOSE { error "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead." } def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "3.0.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def name = image.name def base = name.lastIndexOf('.') != -1 ? name[0..name.lastIndexOf('.') - 1] : name """ @@ -51,7 +51,7 @@ process CELLPOSE { cat <<-END_VERSIONS > versions.yml "${task.process}": - cellpose: $VERSION + cellpose: \$(cellpose --version | awk 'NR==2 {print \$3}') END_VERSIONS """ diff --git a/modules/nf-core/cellpose/meta.yml b/modules/nf-core/cellpose/meta.yml index 433d520..5397944 100644 --- a/modules/nf-core/cellpose/meta.yml +++ b/modules/nf-core/cellpose/meta.yml @@ -6,44 +6,54 @@ keywords: - cellpose tools: - "cellpose": - description: "cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu" + description: "cellpose is an anatomical segmentation algorithm written in Python + 3 by Carsen Stringer and Marius Pachitariu" homepage: "https://github.com/MouseLand/cellpose" documentation: "https://cellpose.readthedocs.io/en/latest/command.html" tool_dev_url: "https://github.com/MouseLand/cellpose" doi: 10.1038/s41592-022-01663-4 licence: ["BSD 3-Clause"] + identifier: biotools:cellpose input: - - meta: - type: map - description: | - Groovy Map containing sample information - (sample id) - - image: - type: file - description: tif file for ready for segmentation - pattern: "*.{tif,tiff}" - - model: - type: file - description: Optional input file. Cellpose 2 model trained by user using human-in-the-loop approach. + - - meta: + type: map + description: | + Groovy Map containing sample information + (sample id) + - image: + type: file + description: tif file for ready for segmentation + pattern: "*.{tif,tiff}" + - - model: + type: file + description: Optional input file. Cellpose 2 model trained by user using human-in-the-loop + approach. output: - - meta: - type: map - description: | - Groovy Map containing sample information - [sample id] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mask: - type: file - description: labelled mask output from cellpose in tif format - pattern: "*.{tif, tiff}" + - meta: + type: map + description: | + Groovy Map containing sample information + [sample id] + - "*masks.tif": + type: file + description: labelled mask output from cellpose in tif format + pattern: "*.{tif, tiff}" - flows: - type: file - description: cell flow output from cellpose - pattern: "*.{tif}" - + - meta: + type: map + description: | + Groovy Map containing sample information + [sample id] + - "*flows.tif": + type: file + description: cell flow output from cellpose + pattern: "*.{tif}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@josenimo" - "@FloWuenne" diff --git a/modules/nf-core/cellpose/tests/main.nf.test b/modules/nf-core/cellpose/tests/main.nf.test index 1b6698d..6a7688b 100644 --- a/modules/nf-core/cellpose/tests/main.nf.test +++ b/modules/nf-core/cellpose/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['imaging']['segmentation']['image'], checkIfExists: true) + file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) ] input[1] = [] """ @@ -44,7 +44,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['imaging']['segmentation']['image'], checkIfExists: true) + file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) ] input[1] = [] """ diff --git a/modules/nf-core/deepcell/mesmer/main.nf b/modules/nf-core/deepcell/mesmer/main.nf index 735a58c..f9b9436 100644 --- a/modules/nf-core/deepcell/mesmer/main.nf +++ b/modules/nf-core/deepcell/mesmer/main.nf @@ -2,7 +2,7 @@ process DEEPCELL_MESMER { tag "$meta.id" label 'process_low' - container "docker.io/wuennemannflorian/deepcell_mesmer:0.4.1_noentry" + container "nf-core/deepcell_mesmer:0.4.1_noentry" input: tuple val(meta) , path(img) diff --git a/modules/nf-core/deepcell/mesmer/meta.yml b/modules/nf-core/deepcell/mesmer/meta.yml index dec360b..0292aa7 100644 --- a/modules/nf-core/deepcell/mesmer/meta.yml +++ b/modules/nf-core/deepcell/mesmer/meta.yml @@ -12,42 +12,44 @@ tools: tool_dev_url: "https://githu/b.com/vanvalenlab/deepcell-tf" doi: 10.1038/s41587-021-01094-0 licence: ["APACHE2"] + identifier: biotools:deepcell input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - img: - type: file - description: Multichannel image file - pattern: "*.{tiff,tif,h5,hdf5}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - membrane_img: - type: file - description: Optional membrane image to be provided separately. - pattern: "*.{tiff,tif,h5,hdf5}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - img: + type: file + description: Multichannel image file + pattern: "*.{tiff,tif,h5,hdf5}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - membrane_img: + type: file + description: Optional membrane image to be provided separately. + pattern: "*.{tiff,tif,h5,hdf5}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - mask: - type: file - description: File containing the mask. - pattern: "*.{tif, tiff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tif": + type: file + description: File containing the mask. + pattern: "*.{tif, tiff}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@migueLib" - "@chiarasch" diff --git a/modules/nf-core/deepcell/mesmer/tests/main.nf.test b/modules/nf-core/deepcell/mesmer/tests/main.nf.test index 9546c1e..d960a54 100644 --- a/modules/nf-core/deepcell/mesmer/tests/main.nf.test +++ b/modules/nf-core/deepcell/mesmer/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { """ input[0] = [ [ id: 'test_img' ], - file(params.test_data['imaging']['segmentation']['image'], checkIfExists: true) + file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) ] input[1] = [ [:], diff --git a/modules/nf-core/ilastik/multicut/environment.yml b/modules/nf-core/ilastik/multicut/environment.yml deleted file mode 100644 index ecd6fa3..0000000 --- a/modules/nf-core/ilastik/multicut/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -name: ilastik_multicut -channels: - - conda-forge - - bioconda - - defaults diff --git a/modules/nf-core/ilastik/multicut/meta.yml b/modules/nf-core/ilastik/multicut/meta.yml index cb2af37..cab8ffa 100644 --- a/modules/nf-core/ilastik/multicut/meta.yml +++ b/modules/nf-core/ilastik/multicut/meta.yml @@ -1,58 +1,66 @@ name: "ilastik_multicut" -description: Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image. +description: Ilastik is a tool that utilizes machine learning algorithms to classify + pixels, segment, track and count cells in images. Ilastik contains a graphical user + interface to interactively label pixels. However, this nextflow module will implement + the --headless mode, to apply pixel classification using a pre-trained .ilp file + on an input image. keywords: - multicut - segmentation - pixel classification tools: - "ilastik": - description: "Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis." + description: "Ilastik is a user friendly tool that enables pixel classification, + segmentation and analysis." homepage: "https://www.ilastik.org/" documentation: "https://www.ilastik.org/documentation/" tool_dev_url: "https://github.com/ilastik/ilastik" - licence: "GPL3" + license: ["GPL3"] + identifier: biotools:ilastik input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - h5: - type: file - description: h5 file containing image stack to classify file - pattern: "*.{h5,hdf5}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ilp: - type: file - description: Trained ilastik .ilp project file - pattern: "*.{ilp}" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - probs: - type: file - description: Probability map for boundary based segmentation - pattern: "*.{h5,,hdf5}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - h5: + type: file + description: h5 file containing image stack to classify file + pattern: "*.{h5,hdf5}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ilp: + type: file + description: Trained ilastik .ilp project file + pattern: "*.{ilp}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - probs: + type: file + description: Probability map for boundary based segmentation + pattern: "*.{h5,,hdf5}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - out_tiff: - type: file - description: Multicut segmentation mask output. - pattern: "*.{tiff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tiff": + type: file + description: Multicut segmentation mask output. + pattern: "*.{tiff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/ilastik/pixelclassification/environment.yml b/modules/nf-core/ilastik/pixelclassification/environment.yml deleted file mode 100644 index a8dafc2..0000000 --- a/modules/nf-core/ilastik/pixelclassification/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -name: ilastik_pixelclassification -channels: - - conda-forge - - bioconda - - defaults diff --git a/modules/nf-core/ilastik/pixelclassification/meta.yml b/modules/nf-core/ilastik/pixelclassification/meta.yml index 6a9e8ba..5d0403b 100644 --- a/modules/nf-core/ilastik/pixelclassification/meta.yml +++ b/modules/nf-core/ilastik/pixelclassification/meta.yml @@ -1,47 +1,55 @@ name: "ilastik_pixelclassification" -description: Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image. +description: Ilastik is a tool that utilizes machine learning algorithms to classify + pixels, segment, track and count cells in images. Ilastik contains a graphical user + interface to interactively label pixels. However, this nextflow module will implement + the --headless mode, to apply pixel classification using a pre-trained .ilp file + on an input image. keywords: - pixel_classification - segmentation - probability_maps tools: - "ilastik": - description: "Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis." + description: "Ilastik is a user friendly tool that enables pixel classification, + segmentation and analysis." homepage: "https://www.ilastik.org/" documentation: "https://www.ilastik.org/documentation/" tool_dev_url: "https://github.com/ilastik/ilastik" - licence: "GPL3" + licence: ["GPL3"] + identifier: biotools:ilastik input: - - meta: - type: map - description: | - Groovy Map containing sample information for h5 file - e.g. [ id:'test', single_end:false ] - - input_img: - type: file - description: Input img file containing image stack to classify - - meta2: - type: map - description: | - Groovy Map containing sample information for ilp file - e.g. [ id:'test', single_end:false ] - - ilp: - type: file - description: Trained ilastik pixel classification .ilp project file - pattern: "*.{ilp}" + - - meta: + type: map + description: | + Groovy Map containing sample information for h5 file + e.g. [ id:'test', single_end:false ] + - input_img: + type: file + description: Input img file containing image stack to classify + - - meta2: + type: map + description: | + Groovy Map containing sample information for ilp file + e.g. [ id:'test', single_end:false ] + - ilp: + type: file + description: Trained ilastik pixel classification .ilp project file + pattern: "*.{ilp}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: Output file from ilastik pixel classification. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${suffix}": + type: file + description: Output file from ilastik pixel classification. + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/mindagap/duplicatefinder/environment.yml b/modules/nf-core/mindagap/duplicatefinder/environment.yml index ad98152..f9b2a1a 100644 --- a/modules/nf-core/mindagap/duplicatefinder/environment.yml +++ b/modules/nf-core/mindagap/duplicatefinder/environment.yml @@ -1,7 +1,7 @@ -name: "MINDAGAP_DUPLICATEFINDER" +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - "bioconda::mindagap=0.0.2" + - bioconda::mindagap=0.0.2 diff --git a/modules/nf-core/mindagap/duplicatefinder/meta.yml b/modules/nf-core/mindagap/duplicatefinder/meta.yml index b92d419..437bdcb 100644 --- a/modules/nf-core/mindagap/duplicatefinder/meta.yml +++ b/modules/nf-core/mindagap/duplicatefinder/meta.yml @@ -6,38 +6,42 @@ keywords: - spatial_transcriptomics tools: - "mindagap": - description: "Takes a single panorama image and fills the empty grid lines with neighbour-weighted values." + description: "Takes a single panorama image and fills the empty grid lines with + neighbour-weighted values." homepage: "https://github.com/ViriatoII/MindaGap/blob/main/README.md" documentation: "https://github.com/ViriatoII/MindaGap/blob/main/README.md" tool_dev_url: "https://github.com/ViriatoII/MindaGap" licence: ["BSD 3-clause License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - spot_table: - type: file - description: tsv file containing one spot per row with order x,y,z,gene without column header. - pattern: "*.{tsv,txt}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - spot_table: + type: file + description: tsv file containing one spot per row with order x,y,z,gene without + column header. + pattern: "*.{tsv,txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - marked_dups_spots: - type: file - description: tsv file containing one spot per row, with duplicated spots labeled with "Duplicated" in their gene column. - pattern: "*.{markedDups.txt}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*markedDups.txt": + type: file + description: tsv file containing one spot per row, with duplicated spots labeled + with "Duplicated" in their gene column. + pattern: "*.{markedDups.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/mindagap/mindagap/environment.yml b/modules/nf-core/mindagap/mindagap/environment.yml index 56fd98b..f9b2a1a 100644 --- a/modules/nf-core/mindagap/mindagap/environment.yml +++ b/modules/nf-core/mindagap/mindagap/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index a27122c..c3b3413 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7a42646..7b7c132 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -38,4 +38,4 @@ }, "timestamp": "2025-01-27T09:30:21.44383553" } -} +} \ No newline at end of file