From 87e23fe7188921367ed445c54e423042c9ccf02b Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 5 Jul 2024 15:34:43 +0200 Subject: [PATCH 1/6] Prevent bioawk overwriting input files if input and module output names are the same --- CHANGELOG.md | 10 ++++++++++ modules.json | 2 +- modules/nf-core/bioawk/environment.yml | 7 +++++++ modules/nf-core/bioawk/main.nf | 4 ++-- modules/nf-core/bioawk/meta.yml | 6 ++---- 5 files changed, 22 insertions(+), 7 deletions(-) create mode 100644 modules/nf-core/bioawk/environment.yml diff --git a/CHANGELOG.md b/CHANGELOG.md index 86a67bc2..19f43b19 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,16 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v1.1.6 - [2024-07-05] + +### `Added` + +### `Fixed` + +- [#XXX](https://github.com/nf-core/funcscan/pull/XXX) Fixed bioawk overwriting input files (❤️ to @Microbion for reporting, fix by @jkfy133) + +### `Dependencies` + ## v1.1.5 - [2024-03-20] ### `Added` diff --git a/modules.json b/modules.json index d4f3ca49..35d0ac17 100644 --- a/modules.json +++ b/modules.json @@ -57,7 +57,7 @@ }, "bioawk": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "dee3479f3b4a828df6052d318403d2b6a87b2d2e", "installed_by": ["modules"], "patch": "modules/nf-core/bioawk/bioawk.diff" }, diff --git a/modules/nf-core/bioawk/environment.yml b/modules/nf-core/bioawk/environment.yml new file mode 100644 index 00000000..5fdfd417 --- /dev/null +++ b/modules/nf-core/bioawk/environment.yml @@ -0,0 +1,7 @@ +name: bioawk +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bioawk=1.0 diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf index bd5c82dd..02f0bbdd 100644 --- a/modules/nf-core/bioawk/main.nf +++ b/modules/nf-core/bioawk/main.nf @@ -2,7 +2,7 @@ process BIOAWK { tag "$meta.id" label 'process_single' - conda "bioconda::bioawk=1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioawk:1.0--h5bf99c6_6': 'biocontainers/bioawk:1.0--h5bf99c6_6' }" @@ -21,7 +21,7 @@ process BIOAWK { script: def args = task.ext.args ?: '' // args is used for the main arguments of the tool prefix = task.ext.prefix ?: "${meta.id}" - + if ("${input}" == "${prefix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" def VERSION = '1.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ bioawk \\ diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml index f0ab564f..c9d00111 100644 --- a/modules/nf-core/bioawk/meta.yml +++ b/modules/nf-core/bioawk/meta.yml @@ -13,9 +13,7 @@ tools: homepage: "https://github.com/lh3/bioawk" documentation: "https://github.com/lh3/bioawk" tool_dev_url: "https://github.com/lh3/bioawk" - licence: "['Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1)']" - input: - meta: type: map @@ -26,7 +24,6 @@ input: type: file description: Input sequence biological sequence file (optionally gzipped) to be manipulated via program specified in `$args`. pattern: "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}" - output: - meta: type: map @@ -43,6 +40,7 @@ output: Manipulated and gzipped version of input sequence file following program specified in `args`. File name will be what is specified in `$prefix`. Do not include `.gz` suffix in `$prefix`! Output files` will be gzipped for you! pattern: "*.gz" - authors: - "@jfy133" +maintainers: + - "@jfy133" From 1bdb2e3a4745112b3763c64bc8bb0ba92c4e761b Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sun, 7 Jul 2024 20:20:42 +0200 Subject: [PATCH 2/6] Fix changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 19f43b19..bf34edde 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#XXX](https://github.com/nf-core/funcscan/pull/XXX) Fixed bioawk overwriting input files (❤️ to @Microbion for reporting, fix by @jkfy133) +- [#396](https://github.com/nf-core/funcscan/pull/396) Fixed bioawk overwriting input files (❤️ to @Microbion for reporting, fix by @jfy133) ### `Dependencies` From b1bb8f013663035bba68223281bdcbdb1a931343 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 8 Jul 2024 10:00:13 +0200 Subject: [PATCH 3/6] Fix docker user group issues --- modules.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules.json b/modules.json index 35d0ac17..f0101971 100644 --- a/modules.json +++ b/modules.json @@ -88,7 +88,7 @@ }, "fargene": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a7231cbccb86535529e33859e05d19ac93f3ea04", "installed_by": ["modules"] }, "gecco/run": { From bd83a343970e51c90f8bbc05710b77f6f254e218 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 8 Jul 2024 10:00:23 +0200 Subject: [PATCH 4/6] Fix docker user issues --- modules/nf-core/fargene/environment.yml | 7 +++++++ modules/nf-core/fargene/main.nf | 2 +- modules/nf-core/fargene/meta.yml | 6 ++---- nextflow.config | 1 + 4 files changed, 11 insertions(+), 5 deletions(-) create mode 100644 modules/nf-core/fargene/environment.yml diff --git a/modules/nf-core/fargene/environment.yml b/modules/nf-core/fargene/environment.yml new file mode 100644 index 00000000..56629ff4 --- /dev/null +++ b/modules/nf-core/fargene/environment.yml @@ -0,0 +1,7 @@ +name: fargene +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fargene=0.1 diff --git a/modules/nf-core/fargene/main.nf b/modules/nf-core/fargene/main.nf index b0f6c183..b2feb86a 100644 --- a/modules/nf-core/fargene/main.nf +++ b/modules/nf-core/fargene/main.nf @@ -3,7 +3,7 @@ process FARGENE { label 'process_low' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::fargene=0.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4' : 'biocontainers/fargene:0.1--py27h21c881e_4' }" diff --git a/modules/nf-core/fargene/meta.yml b/modules/nf-core/fargene/meta.yml index fffc88c1..8f1540b1 100644 --- a/modules/nf-core/fargene/meta.yml +++ b/modules/nf-core/fargene/meta.yml @@ -12,9 +12,7 @@ tools: homepage: https://github.com/fannyhb/fargene documentation: https://github.com/fannyhb/fargene tool_dev_url: https://github.com/fannyhb/fargene - licence: ["MIT"] - input: - meta: type: map @@ -28,7 +26,6 @@ input: - hmm_model: type: string description: name of custom hidden markov model to be used [pre-defined class_a, class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, tet_enzyme] - output: - meta: type: map @@ -95,6 +92,7 @@ output: type: file description: The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used. pattern: "*.{fasta}" - authors: - "@louperelo" +maintainers: + - "@louperelo" diff --git a/nextflow.config b/nextflow.config index fe5ded07..5d8d969a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -269,6 +269,7 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false + docker.runOptions = '-u $(id -u):$(id -g)' } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' From 766f4b027e10fea0c5d85d03d2eeb0d1e8961b50 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 8 Jul 2024 14:09:51 +0200 Subject: [PATCH 5/6] Update CHANGELOG.md Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bf34edde..e8c0244a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#396](https://github.com/nf-core/funcscan/pull/396) Fixed bioawk overwriting input files (❤️ to @Microbion for reporting, fix by @jfy133) +- [#396](https://github.com/nf-core/funcscan/pull/396) Fixed bioawk overwriting input files. (❤️ to @Microbion for reporting, fix by @jfy133) ### `Dependencies` From d9684236f2c9efa4993502a553b09ed42788a6ba Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 8 Jul 2024 14:10:33 +0200 Subject: [PATCH 6/6] Apply suggestions from code review --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e8c0244a..5eff7c3a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.1.6 - [2024-07-05] +## v1.1.6 - [2024-07-08] ### `Added`