From 51a0cc84df539a70b578178a5a486c442a72cd00 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Fri, 8 Dec 2023 14:30:23 +0100 Subject: [PATCH 1/4] Update a few module versions + environment.ymls --- CHANGELOG.md | 4 +- modules.json | 68 +++++++++---------- modules/nf-core/abricate/run/environment.yml | 1 + modules/nf-core/ampcombi/environment.yml | 1 + modules/nf-core/ampir/environment.yml | 1 + .../nf-core/amplify/predict/environment.yml | 1 + modules/nf-core/amplify/predict/meta.yml | 2 +- .../nf-core/amrfinderplus/run/environment.yml | 1 + .../amrfinderplus/update/environment.yml | 1 + .../antismash/antismashlite/environment.yml | 1 + .../environment.yml | 1 + modules/nf-core/bakta/bakta/environment.yml | 1 + .../bakta/baktadbdownload/environment.yml | 1 + modules/nf-core/bioawk/environment.yml | 1 + .../dumpsoftwareversions/environment.yml | 1 + .../custom/dumpsoftwareversions/meta.yml | 2 +- .../deeparg/downloaddata/environment.yml | 3 +- modules/nf-core/deeparg/downloaddata/main.nf | 11 ++- modules/nf-core/deeparg/downloaddata/meta.yml | 6 +- .../nf-core/deeparg/predict/environment.yml | 3 +- modules/nf-core/deeparg/predict/main.nf | 14 +++- modules/nf-core/deeparg/predict/meta.yml | 6 +- .../nf-core/deepbgc/download/environment.yml | 3 +- modules/nf-core/deepbgc/download/main.nf | 4 +- modules/nf-core/deepbgc/download/meta.yml | 2 +- .../nf-core/deepbgc/pipeline/environment.yml | 3 +- modules/nf-core/deepbgc/pipeline/main.nf | 4 +- modules/nf-core/deepbgc/pipeline/meta.yml | 2 +- modules/nf-core/fargene/environment.yml | 1 + modules/nf-core/gecco/run/environment.yml | 1 + modules/nf-core/gunzip/environment.yml | 1 + .../hamronization/abricate/environment.yml | 1 + .../amrfinderplus/environment.yml | 1 + .../hamronization/deeparg/environment.yml | 1 + .../hamronization/fargene/environment.yml | 1 + .../nf-core/hamronization/rgi/environment.yml | 1 + .../hamronization/summarize/environment.yml | 1 + .../nf-core/hmmer/hmmsearch/environment.yml | 1 + .../nf-core/macrel/contigs/environment.yml | 1 + modules/nf-core/multiqc/environment.yml | 3 +- modules/nf-core/multiqc/main.nf | 6 +- modules/nf-core/multiqc/meta.yml | 4 +- modules/nf-core/prodigal/environment.yml | 1 + modules/nf-core/prokka/environment.yml | 1 + modules/nf-core/pyrodigal/environment.yml | 1 + modules/nf-core/rgi/main/environment.yml | 1 + modules/nf-core/tabix/bgzip/environment.yml | 1 + modules/nf-core/untar/environment.yml | 1 + 48 files changed, 116 insertions(+), 63 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ab5e0f34..8c0f87dc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Tool | Previous version | New version | | ------- | ---------------- | ----------- | -| MultiQC | 1.15 | 1.17 | +| DeepARG | 1.0.2 | 1.0.4 | +| DeepBGC | 0.1.30 | 0.1.31 | +| MultiQC | 1.15 | 1.18 | ### `Deprecated` diff --git a/modules.json b/modules.json index bbcf1156..e4515115 100644 --- a/modules.json +++ b/modules.json @@ -7,173 +7,173 @@ "nf-core": { "abricate/run": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "ampcombi": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "ampir": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "amplify/predict": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "b15e8f066db9071996e83c0bec4a5d1a6e0b7b65", "installed_by": ["modules"] }, "amrfinderplus/run": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "amrfinderplus/update": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "antismash/antismashlite": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "antismash/antismashlitedownloaddatabases": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "bakta/bakta": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "bakta/baktadbdownload": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "bioawk": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"], "patch": "modules/nf-core/bioawk/bioawk.diff" }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "fc6caedab1c71113aa440900e5989dd1c03ec58f", + "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", "installed_by": ["modules"] }, "deeparg/downloaddata": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "5da7b7e8d3b1249942a1030c412059170b95e925", "installed_by": ["modules"] }, "deeparg/predict": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "5da7b7e8d3b1249942a1030c412059170b95e925", "installed_by": ["modules"] }, "deepbgc/download": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "f315f85d9ac6c321f6e3596493fd61019340df2a", "installed_by": ["modules"] }, "deepbgc/pipeline": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "f315f85d9ac6c321f6e3596493fd61019340df2a", "installed_by": ["modules"] }, "fargene": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "2506084773f9fa01b65b25058cd5a010f87395b4", "installed_by": ["modules"] }, "gecco/run": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gunzip": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "hamronization/abricate": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "hamronization/amrfinderplus": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "hamronization/deeparg": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "hamronization/fargene": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "hamronization/rgi": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "hamronization/summarize": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "hmmer/hmmsearch": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "macrel/contigs": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "4ab13872435962dadc239979554d13709e20bf29", "installed_by": ["modules"] }, "prodigal": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "prokka": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "pyrodigal": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "rgi/main": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "tabix/bgzip": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] } } diff --git a/modules/nf-core/abricate/run/environment.yml b/modules/nf-core/abricate/run/environment.yml index 845f27e6..4b2a1d2a 100644 --- a/modules/nf-core/abricate/run/environment.yml +++ b/modules/nf-core/abricate/run/environment.yml @@ -1,3 +1,4 @@ +name: abricate_run channels: - conda-forge - bioconda diff --git a/modules/nf-core/ampcombi/environment.yml b/modules/nf-core/ampcombi/environment.yml index 32e17786..a388a034 100644 --- a/modules/nf-core/ampcombi/environment.yml +++ b/modules/nf-core/ampcombi/environment.yml @@ -1,3 +1,4 @@ +name: ampcombi channels: - conda-forge - bioconda diff --git a/modules/nf-core/ampir/environment.yml b/modules/nf-core/ampir/environment.yml index 8e55db05..8cb475d1 100644 --- a/modules/nf-core/ampir/environment.yml +++ b/modules/nf-core/ampir/environment.yml @@ -1,3 +1,4 @@ +name: ampir channels: - conda-forge - bioconda diff --git a/modules/nf-core/amplify/predict/environment.yml b/modules/nf-core/amplify/predict/environment.yml index e674fc1a..56b0ab6d 100644 --- a/modules/nf-core/amplify/predict/environment.yml +++ b/modules/nf-core/amplify/predict/environment.yml @@ -1,3 +1,4 @@ +name: amplify_predict channels: - conda-forge - bioconda diff --git a/modules/nf-core/amplify/predict/meta.yml b/modules/nf-core/amplify/predict/meta.yml index e6658aa9..5ef93c83 100644 --- a/modules/nf-core/amplify/predict/meta.yml +++ b/modules/nf-core/amplify/predict/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/bcgsc/AMPlify" tool_dev_url: "https://github.com/bcgsc/AMPlify" doi: "10.1186/s12864-022-08310-4" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/amrfinderplus/run/environment.yml b/modules/nf-core/amrfinderplus/run/environment.yml index ee19ed01..b5e3b4fc 100644 --- a/modules/nf-core/amrfinderplus/run/environment.yml +++ b/modules/nf-core/amrfinderplus/run/environment.yml @@ -1,3 +1,4 @@ +name: amrfinderplus_run channels: - conda-forge - bioconda diff --git a/modules/nf-core/amrfinderplus/update/environment.yml b/modules/nf-core/amrfinderplus/update/environment.yml index ee19ed01..37001845 100644 --- a/modules/nf-core/amrfinderplus/update/environment.yml +++ b/modules/nf-core/amrfinderplus/update/environment.yml @@ -1,3 +1,4 @@ +name: amrfinderplus_update channels: - conda-forge - bioconda diff --git a/modules/nf-core/antismash/antismashlite/environment.yml b/modules/nf-core/antismash/antismashlite/environment.yml index ced2ff17..76de944b 100644 --- a/modules/nf-core/antismash/antismashlite/environment.yml +++ b/modules/nf-core/antismash/antismashlite/environment.yml @@ -1,3 +1,4 @@ +name: antismash_antismashlite channels: - conda-forge - bioconda diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml b/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml index ced2ff17..e6288d56 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml @@ -1,3 +1,4 @@ +name: antismash_antismashlitedownloaddatabases channels: - conda-forge - bioconda diff --git a/modules/nf-core/bakta/bakta/environment.yml b/modules/nf-core/bakta/bakta/environment.yml index 102348df..07a11d86 100644 --- a/modules/nf-core/bakta/bakta/environment.yml +++ b/modules/nf-core/bakta/bakta/environment.yml @@ -1,3 +1,4 @@ +name: bakta_bakta channels: - conda-forge - bioconda diff --git a/modules/nf-core/bakta/baktadbdownload/environment.yml b/modules/nf-core/bakta/baktadbdownload/environment.yml index 102348df..08136465 100644 --- a/modules/nf-core/bakta/baktadbdownload/environment.yml +++ b/modules/nf-core/bakta/baktadbdownload/environment.yml @@ -1,3 +1,4 @@ +name: bakta_baktadbdownload channels: - conda-forge - bioconda diff --git a/modules/nf-core/bioawk/environment.yml b/modules/nf-core/bioawk/environment.yml index 33315d10..5fdfd417 100644 --- a/modules/nf-core/bioawk/environment.yml +++ b/modules/nf-core/bioawk/environment.yml @@ -1,3 +1,4 @@ +name: bioawk channels: - conda-forge - bioconda diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index 9d0e6b20..f0c63f69 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -1,3 +1,4 @@ +name: custom_dumpsoftwareversions channels: - conda-forge - bioconda diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index 9414c32d..5f15a5fd 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: diff --git a/modules/nf-core/deeparg/downloaddata/environment.yml b/modules/nf-core/deeparg/downloaddata/environment.yml index 5df51cdb..87435be5 100644 --- a/modules/nf-core/deeparg/downloaddata/environment.yml +++ b/modules/nf-core/deeparg/downloaddata/environment.yml @@ -1,6 +1,7 @@ +name: deeparg_downloaddata channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::deeparg=1.0.2 + - bioconda::deeparg=1.0.4 diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index ea0aa30a..0bc7a74a 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -3,8 +3,8 @@ process DEEPARG_DOWNLOADDATA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : - 'biocontainers/deeparg:1.0.2--pyhdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/deeparg:1.0.4--pyhdfd78af_0' : + 'biocontainers/deeparg:1.0.4--pyhdfd78af_0' }" /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 @@ -25,6 +25,13 @@ process DEEPARG_DOWNLOADDATA { def args = task.ext.args ?: '' def VERSION='1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ + + # Theano needs a writable space and uses the home directory by default, + # but the latter is not always writable, for instance when Singularity + # is run in --no-home mode + mkdir -p theano + export THEANO_FLAGS="base_compiledir=\$PWD/theano" + deeparg \\ download_data \\ $args \\ diff --git a/modules/nf-core/deeparg/downloaddata/meta.yml b/modules/nf-core/deeparg/downloaddata/meta.yml index 2d8a3de6..65fb3903 100644 --- a/modules/nf-core/deeparg/downloaddata/meta.yml +++ b/modules/nf-core/deeparg/downloaddata/meta.yml @@ -10,9 +10,9 @@ keywords: tools: - deeparg: description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes - homepage: https://bench.cs.vt.edu/deeparg - documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/ - tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/ + homepage: https://github.com/gaarangoa/deeparg + documentation: https://github.com/gaarangoa/deeparg + tool_dev_url: https://github.com/gaarangoa/deeparg doi: "10.1186/s40168-018-0401-z" licence: ["MIT"] # No input required for download module. diff --git a/modules/nf-core/deeparg/predict/environment.yml b/modules/nf-core/deeparg/predict/environment.yml index 5df51cdb..aa686701 100644 --- a/modules/nf-core/deeparg/predict/environment.yml +++ b/modules/nf-core/deeparg/predict/environment.yml @@ -1,6 +1,7 @@ +name: deeparg_predict channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::deeparg=1.0.2 + - bioconda::deeparg=1.0.4 diff --git a/modules/nf-core/deeparg/predict/main.nf b/modules/nf-core/deeparg/predict/main.nf index 17a3f1c1..895b8e4e 100644 --- a/modules/nf-core/deeparg/predict/main.nf +++ b/modules/nf-core/deeparg/predict/main.nf @@ -4,8 +4,8 @@ process DEEPARG_PREDICT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : - 'biocontainers/deeparg:1.0.2--pyhdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/deeparg:1.0.4--pyhdfd78af_0' : + 'biocontainers/deeparg:1.0.4--pyhdfd78af_0' }" /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 @@ -31,12 +31,20 @@ process DEEPARG_PREDICT { def prefix = task.ext.prefix ?: "${meta.id}" def VERSION='1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ + DATABASE=`find -L $db -type d -name "database" | sed 's/database//'` + + # Theano needs a writable space and uses the home directory by default, + # but the latter is not always writable, for instance when Singularity + # is run in --no-home mode + mkdir -p theano + export THEANO_FLAGS="base_compiledir=\$PWD/theano" + deeparg \\ predict \\ $args \\ -i $fasta \\ -o ${prefix} \\ - -d $db \\ + -d \$DATABASE \\ --model $model cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/deeparg/predict/meta.yml b/modules/nf-core/deeparg/predict/meta.yml index 613da293..d62c2c5f 100644 --- a/modules/nf-core/deeparg/predict/meta.yml +++ b/modules/nf-core/deeparg/predict/meta.yml @@ -12,9 +12,9 @@ keywords: tools: - deeparg: description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes - homepage: https://bench.cs.vt.edu/deeparg - documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/ - tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/ + homepage: https://github.com/gaarangoa/deeparg + documentation: https://github.com/gaarangoa/deeparg + tool_dev_url: https://github.com/gaarangoa/deeparg doi: "10.1186/s40168-018-0401-z" licence: ["MIT"] input: diff --git a/modules/nf-core/deepbgc/download/environment.yml b/modules/nf-core/deepbgc/download/environment.yml index 8cf40456..84d467f0 100644 --- a/modules/nf-core/deepbgc/download/environment.yml +++ b/modules/nf-core/deepbgc/download/environment.yml @@ -1,6 +1,7 @@ +name: deepbgc_download channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::deepbgc=0.1.30 + - bioconda::deepbgc=0.1.31 diff --git a/modules/nf-core/deepbgc/download/main.nf b/modules/nf-core/deepbgc/download/main.nf index 56542639..b141142c 100644 --- a/modules/nf-core/deepbgc/download/main.nf +++ b/modules/nf-core/deepbgc/download/main.nf @@ -3,8 +3,8 @@ process DEEPBGC_DOWNLOAD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1': - 'biocontainers/deepbgc:0.1.30--pyhb7b1952_1' }" + 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.31--pyhca03a8a_0': + 'biocontainers/deepbgc:0.1.31--pyhca03a8a_0' }" output: path "deepbgc_db/" , emit: db diff --git a/modules/nf-core/deepbgc/download/meta.yml b/modules/nf-core/deepbgc/download/meta.yml index 51476203..6444dd41 100644 --- a/modules/nf-core/deepbgc/download/meta.yml +++ b/modules/nf-core/deepbgc/download/meta.yml @@ -18,7 +18,7 @@ tools: documentation: "https://github.com/Merck/deepbgc" tool_dev_url: "https://github.com/Merck/deepbgc" doi: "10.1093/nar/gkz654" - licence: "['MIT']" + licence: ["MIT"] output: - versions: type: file diff --git a/modules/nf-core/deepbgc/pipeline/environment.yml b/modules/nf-core/deepbgc/pipeline/environment.yml index 8cf40456..fe0087a2 100644 --- a/modules/nf-core/deepbgc/pipeline/environment.yml +++ b/modules/nf-core/deepbgc/pipeline/environment.yml @@ -1,6 +1,7 @@ +name: deepbgc_pipeline channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::deepbgc=0.1.30 + - bioconda::deepbgc=0.1.31 diff --git a/modules/nf-core/deepbgc/pipeline/main.nf b/modules/nf-core/deepbgc/pipeline/main.nf index e3544b34..9cc22708 100644 --- a/modules/nf-core/deepbgc/pipeline/main.nf +++ b/modules/nf-core/deepbgc/pipeline/main.nf @@ -4,8 +4,8 @@ process DEEPBGC_PIPELINE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1': - 'biocontainers/deepbgc:0.1.30--pyhb7b1952_1' }" + 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.31--pyhca03a8a_0': + 'biocontainers/deepbgc:0.1.31--pyhca03a8a_0' }" input: tuple val(meta), path(genome) diff --git a/modules/nf-core/deepbgc/pipeline/meta.yml b/modules/nf-core/deepbgc/pipeline/meta.yml index 20f3a6f8..6c29cebc 100644 --- a/modules/nf-core/deepbgc/pipeline/meta.yml +++ b/modules/nf-core/deepbgc/pipeline/meta.yml @@ -16,7 +16,7 @@ tools: documentation: "https://github.com/Merck/deepbgc" tool_dev_url: "https://github.com/Merck/deepbgc" doi: "10.1093/nar/gkz654" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/fargene/environment.yml b/modules/nf-core/fargene/environment.yml index eacce9bf..56629ff4 100644 --- a/modules/nf-core/fargene/environment.yml +++ b/modules/nf-core/fargene/environment.yml @@ -1,3 +1,4 @@ +name: fargene channels: - conda-forge - bioconda diff --git a/modules/nf-core/gecco/run/environment.yml b/modules/nf-core/gecco/run/environment.yml index 83581278..b4b8355b 100644 --- a/modules/nf-core/gecco/run/environment.yml +++ b/modules/nf-core/gecco/run/environment.yml @@ -1,3 +1,4 @@ +name: gecco_run channels: - conda-forge - bioconda diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index 222b301f..25910b34 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -1,3 +1,4 @@ +name: gunzip channels: - conda-forge - bioconda diff --git a/modules/nf-core/hamronization/abricate/environment.yml b/modules/nf-core/hamronization/abricate/environment.yml index 0a083ec3..0d7c0e66 100644 --- a/modules/nf-core/hamronization/abricate/environment.yml +++ b/modules/nf-core/hamronization/abricate/environment.yml @@ -1,3 +1,4 @@ +name: hamronization_abricate channels: - conda-forge - bioconda diff --git a/modules/nf-core/hamronization/amrfinderplus/environment.yml b/modules/nf-core/hamronization/amrfinderplus/environment.yml index 0a083ec3..c462be8e 100644 --- a/modules/nf-core/hamronization/amrfinderplus/environment.yml +++ b/modules/nf-core/hamronization/amrfinderplus/environment.yml @@ -1,3 +1,4 @@ +name: hamronization_amrfinderplus channels: - conda-forge - bioconda diff --git a/modules/nf-core/hamronization/deeparg/environment.yml b/modules/nf-core/hamronization/deeparg/environment.yml index 0a083ec3..86f99233 100644 --- a/modules/nf-core/hamronization/deeparg/environment.yml +++ b/modules/nf-core/hamronization/deeparg/environment.yml @@ -1,3 +1,4 @@ +name: hamronization_deeparg channels: - conda-forge - bioconda diff --git a/modules/nf-core/hamronization/fargene/environment.yml b/modules/nf-core/hamronization/fargene/environment.yml index 0a083ec3..4f5a7557 100644 --- a/modules/nf-core/hamronization/fargene/environment.yml +++ b/modules/nf-core/hamronization/fargene/environment.yml @@ -1,3 +1,4 @@ +name: hamronization_fargene channels: - conda-forge - bioconda diff --git a/modules/nf-core/hamronization/rgi/environment.yml b/modules/nf-core/hamronization/rgi/environment.yml index 0a083ec3..6fa71205 100644 --- a/modules/nf-core/hamronization/rgi/environment.yml +++ b/modules/nf-core/hamronization/rgi/environment.yml @@ -1,3 +1,4 @@ +name: hamronization_rgi channels: - conda-forge - bioconda diff --git a/modules/nf-core/hamronization/summarize/environment.yml b/modules/nf-core/hamronization/summarize/environment.yml index 0a083ec3..0f8f05d3 100644 --- a/modules/nf-core/hamronization/summarize/environment.yml +++ b/modules/nf-core/hamronization/summarize/environment.yml @@ -1,3 +1,4 @@ +name: hamronization_summarize channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmer/hmmsearch/environment.yml b/modules/nf-core/hmmer/hmmsearch/environment.yml index e4787ce5..89978984 100644 --- a/modules/nf-core/hmmer/hmmsearch/environment.yml +++ b/modules/nf-core/hmmer/hmmsearch/environment.yml @@ -1,3 +1,4 @@ +name: hmmer_hmmsearch channels: - conda-forge - bioconda diff --git a/modules/nf-core/macrel/contigs/environment.yml b/modules/nf-core/macrel/contigs/environment.yml index 20d2762d..e6c11226 100644 --- a/modules/nf-core/macrel/contigs/environment.yml +++ b/modules/nf-core/macrel/contigs/environment.yml @@ -1,3 +1,4 @@ +name: macrel_contigs channels: - conda-forge - bioconda diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 9d0e6b20..bc0bdb5b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,6 +1,7 @@ +name: multiqc channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::multiqc=1.17 + - bioconda::multiqc=1.18 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 2bbc3983..00cc48d2 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : - 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' : + 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -25,12 +25,14 @@ process MULTIQC { def args = task.ext.args ?: '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' """ multiqc \\ --force \\ $args \\ $config \\ $extra_config \\ + $logo \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index a61223ed..f1aa660e 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,5 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: MultiQC +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC diff --git a/modules/nf-core/prodigal/environment.yml b/modules/nf-core/prodigal/environment.yml index 05ca3ba0..85746534 100644 --- a/modules/nf-core/prodigal/environment.yml +++ b/modules/nf-core/prodigal/environment.yml @@ -1,3 +1,4 @@ +name: prodigal channels: - conda-forge - bioconda diff --git a/modules/nf-core/prokka/environment.yml b/modules/nf-core/prokka/environment.yml index b59d6c32..d7c44d5a 100644 --- a/modules/nf-core/prokka/environment.yml +++ b/modules/nf-core/prokka/environment.yml @@ -1,3 +1,4 @@ +name: prokka channels: - conda-forge - bioconda diff --git a/modules/nf-core/pyrodigal/environment.yml b/modules/nf-core/pyrodigal/environment.yml index 5675b387..8d3107b9 100644 --- a/modules/nf-core/pyrodigal/environment.yml +++ b/modules/nf-core/pyrodigal/environment.yml @@ -1,3 +1,4 @@ +name: pyrodigal channels: - conda-forge - bioconda diff --git a/modules/nf-core/rgi/main/environment.yml b/modules/nf-core/rgi/main/environment.yml index 0457b82b..f4eeef95 100644 --- a/modules/nf-core/rgi/main/environment.yml +++ b/modules/nf-core/rgi/main/environment.yml @@ -1,3 +1,4 @@ +name: rgi_main channels: - conda-forge - bioconda diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index fdd84057..4fe40c56 100644 --- a/modules/nf-core/tabix/bgzip/environment.yml +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -1,3 +1,4 @@ +name: tabix_bgzip channels: - conda-forge - bioconda diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 2d52ce64..d6917da3 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,3 +1,4 @@ +name: untar channels: - conda-forge - bioconda From 00d95673009830858999716e195de8cf86898557 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Fri, 8 Dec 2023 15:05:13 +0100 Subject: [PATCH 2/4] Remove separate DeepARG test profile --- conf/test.config | 2 -- conf/test_deeparg.config | 38 -------------------------------------- 2 files changed, 40 deletions(-) delete mode 100644 conf/test_deeparg.config diff --git a/conf/test.config b/conf/test.config index ffd6a39e..797e2935 100644 --- a/conf/test.config +++ b/conf/test.config @@ -29,8 +29,6 @@ params { arg_fargene_hmmmodel = 'class_a,class_b_1_2' // Database download regularly fails due to server downtime // Tested instead with -profile test_deeparg to allow checking of other tools - arg_skip_deeparg = true - run_amp_screening = true } diff --git a/conf/test_deeparg.config b/conf/test_deeparg.config deleted file mode 100644 index ff229340..00000000 --- a/conf/test_deeparg.config +++ /dev/null @@ -1,38 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run nf-core/funcscan -profile test_deeparg, --outdir - - This executes DeepARG separately due to regular flakiness in database download server - ----------------------------------------------------------------------------------------- -*/ - -params { - config_profile_name = 'DeepARG test profile' - config_profile_description = 'Minimal test dataset to check DeepARG ARG screening function' - - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - - // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet.csv' - - annotation_tool = 'prodigal' - - run_arg_screening = true - arg_skip_fargene = true - arg_skip_rgi = true - arg_skip_amrfinderplus = true - arg_skip_abricate = true - arg_skip_deeparg = false - - run_amp_screening = false - run_bgc_screening = false -} From 69b7a461f411a6149e9d9295d420b0d19b4d630d Mon Sep 17 00:00:00 2001 From: jasmezz Date: Fri, 8 Dec 2023 15:07:45 +0100 Subject: [PATCH 3/4] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8c0f87dc..d7e9d9c5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` - [#322](https://github.com/nf-core/funcscan/pull/322) Updated all modules: introduce environment.yml files. (by @jasmezz) +- [#324](https://github.com/nf-core/funcscan/pull/324) Removed separate DeepARG test profile because database download is now stable. (by @jasmezz) ### `Fixed` From 38c9787b988ddb02428284e157527335739b8a61 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Fri, 8 Dec 2023 15:44:29 +0100 Subject: [PATCH 4/4] Update deeparg module (version report) [skip ci] --- modules.json | 4 ++-- modules/nf-core/deeparg/downloaddata/main.nf | 2 +- modules/nf-core/deeparg/predict/main.nf | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules.json b/modules.json index e4515115..7d0e6f70 100644 --- a/modules.json +++ b/modules.json @@ -68,12 +68,12 @@ }, "deeparg/downloaddata": { "branch": "master", - "git_sha": "5da7b7e8d3b1249942a1030c412059170b95e925", + "git_sha": "045be63d4c76c2cf4e7ca263e8c2b5fbce2ab070", "installed_by": ["modules"] }, "deeparg/predict": { "branch": "master", - "git_sha": "5da7b7e8d3b1249942a1030c412059170b95e925", + "git_sha": "045be63d4c76c2cf4e7ca263e8c2b5fbce2ab070", "installed_by": ["modules"] }, "deepbgc/download": { diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index 0bc7a74a..f5688b96 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -23,7 +23,7 @@ process DEEPARG_DOWNLOADDATA { script: def args = task.ext.args ?: '' - def VERSION='1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION='1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ # Theano needs a writable space and uses the home directory by default, diff --git a/modules/nf-core/deeparg/predict/main.nf b/modules/nf-core/deeparg/predict/main.nf index 895b8e4e..4fca811d 100644 --- a/modules/nf-core/deeparg/predict/main.nf +++ b/modules/nf-core/deeparg/predict/main.nf @@ -29,7 +29,7 @@ process DEEPARG_PREDICT { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION='1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION='1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ DATABASE=`find -L $db -type d -name "database" | sed 's/database//'`