Fix modules warned or failed with nf-core modules lint (#1191)

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Harshil Patel 2022-01-03 18:00:46 +00:00 committed by GitHub
parent c0e1489133
commit e3285528ac
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16 changed files with 22 additions and 16 deletions

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@ -5,7 +5,7 @@ process ATAQV_ATAQV {
conda (params.enable_conda ? "bioconda::ataqv=1.2.1" : null) conda (params.enable_conda ? "bioconda::ataqv=1.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ataqv:1.2.1--py39ha23c084_2' : 'https://depot.galaxyproject.org/singularity/ataqv:1.2.1--py39ha23c084_2' :
'quay.io/biocontainers/ataqv:1.2.1--py36hfdecbe1_2' }" 'quay.io/biocontainers/ataqv:1.2.1--py39ha23c084_2' }"
input: input:
tuple val(meta), path(bam), path(bai), path(peak_file) tuple val(meta), path(bam), path(bai), path(peak_file)

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@ -13,7 +13,7 @@ process BCFTOOLS_INDEX {
output: output:
tuple val(meta), path("*.csi"), optional:true, emit: csi tuple val(meta), path("*.csi"), optional:true, emit: csi
tuple val(meta), path("*.tbi"), optional:true, emit: tbi tuple val(meta), path("*.tbi"), optional:true, emit: tbi
path "versions.yml" , emit: version path "versions.yml" , emit: versions
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''

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@ -5,7 +5,7 @@ process BOWTIE2_BUILD {
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' : 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
'quay.io/biocontainers/bowtie2:2.4.4--py36hd4290be_0' }" 'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
input: input:
path fasta path fasta

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@ -5,7 +5,7 @@ process CUTADAPT {
conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null) conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1' : 'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1' :
'quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1' }" 'quay.io/biocontainers/cutadapt:3.4--py39h38f01e4_1' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)

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@ -13,7 +13,7 @@ process FGBIO_FASTQTOBAM {
output: output:
tuple val(meta), path("*_umi_converted.bam"), emit: umibam tuple val(meta), path("*_umi_converted.bam"), emit: umibam
path "versions.yml" , emit: version path "versions.yml" , emit: versions
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''

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@ -2,6 +2,7 @@ def VERSION = '1.5.0' // Version information not provided by tool on CLI
process GTDBTK_CLASSIFYWF { process GTDBTK_CLASSIFYWF {
tag "${meta.assembler}-${meta.id}" tag "${meta.assembler}-${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null) conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

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@ -5,7 +5,7 @@ process IDR {
conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null) conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' : 'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' :
'quay.io/biocontainers/idr:2.0.4.2--py38h9af456f_5' }" 'quay.io/biocontainers/idr:2.0.4.2--py39hcbe4a3b_5' }"
input: input:
path peaks path peaks

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@ -9,7 +9,7 @@ process JUPYTERNOTEBOOK {
//ipykernel, jupytext, papermill and nbconvert Python packages. //ipykernel, jupytext, papermill and nbconvert Python packages.
conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null) conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963%3A879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' :
'quay.io/biocontainers/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' }" 'quay.io/biocontainers/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' }"
input: input:

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@ -8,8 +8,6 @@ process KRONA_KRONADB {
'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' : 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' :
'quay.io/biocontainers/krona:2.7.1--pl526_5' }" 'quay.io/biocontainers/krona:2.7.1--pl526_5' }"
input:
output: output:
path 'taxonomy/taxonomy.tab', emit: db path 'taxonomy/taxonomy.tab', emit: db
path "versions.yml" , emit: versions path "versions.yml" , emit: versions

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@ -1,6 +1,5 @@
process MALT_RUN { process MALT_RUN {
label 'process_high'
label 'process_high_memory'
conda (params.enable_conda ? "bioconda::malt=0.53" : null) conda (params.enable_conda ? "bioconda::malt=0.53" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

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@ -6,7 +6,7 @@ process PARACLU {
conda (params.enable_conda ? "bioconda::paraclu=10" : null) conda (params.enable_conda ? "bioconda::paraclu=10" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/paraclu%3A10--h9a82719_1' : 'https://depot.galaxyproject.org/singularity/paraclu:10--h9a82719_1' :
'quay.io/biocontainers/paraclu:10--h9a82719_1' }" 'quay.io/biocontainers/paraclu:10--h9a82719_1' }"
input: input:

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@ -4,7 +4,7 @@ process PIRATE {
conda (params.enable_conda ? "bioconda::pirate=1.0.4" : null) conda (params.enable_conda ? "bioconda::pirate=1.0.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pirate%3A1.0.4--hdfd78af_1' : 'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_1' :
'quay.io/biocontainers/pirate:1.0.4--hdfd78af_1' }" 'quay.io/biocontainers/pirate:1.0.4--hdfd78af_1' }"
input: input:

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@ -5,7 +5,7 @@ process PORECHOP {
conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null) conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' : 'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' :
'quay.io/biocontainers/porechop:0.2.4--py38h8c62d01_2' }" 'quay.io/biocontainers/porechop:0.2.4--py39h7cff6ad_2' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)

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@ -9,7 +9,7 @@ process RMARKDOWNNOTEBOOK {
//yaml and rmarkdown R packages. //yaml and rmarkdown R packages.
conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null) conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5%3A0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' :
'quay.io/biocontainers/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' }" 'quay.io/biocontainers/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' }"
input: input:

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@ -4,7 +4,7 @@ process SPATYPER {
conda (params.enable_conda ? "bioconda::spatyper=0.3.3" : null) conda (params.enable_conda ? "bioconda::spatyper=0.3.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/spatyper%3A0.3.3--pyhdfd78af_3' : 'https://depot.galaxyproject.org/singularity/spatyper:0.3.3--pyhdfd78af_3' :
'quay.io/biocontainers/spatyper:0.3.3--pyhdfd78af_3' }" 'quay.io/biocontainers/spatyper:0.3.3--pyhdfd78af_3' }"
input: input:

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@ -282,6 +282,14 @@ cellranger/gtf:
- modules/cellranger/gtf/** - modules/cellranger/gtf/**
- tests/modules/cellranger/gtf/** - tests/modules/cellranger/gtf/**
cellranger/mkfastq:
- modules/cellranger/mkfastq/**
- tests/modules/cellranger/mkfastq/**
cellranger/mkgtf:
- modules/cellranger/mkgtf/**
- tests/modules/cellranger/mkgtf/**
cellranger/mkref: cellranger/mkref:
- modules/cellranger/mkref/** - modules/cellranger/mkref/**
- tests/modules/cellranger/mkref/** - tests/modules/cellranger/mkref/**