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Merge branch 'sep-krakenuniq-test' of github.com:nf-core/taxprofiler into sep-krakenuniq-test

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This commit is contained in:
James Fellows Yates 2022-12-02 12:48:18 +01:00
commit a3cd188b1f
13 changed files with 44 additions and 20 deletions
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9
conf/modules.config
View file

@ -281,7 +281,7 @@ process {
}
withName: MALT_RUN {
ext.args = { "${meta.db_params}" }
ext.args = { "${meta.db_params} -m ${params.malt_mode}" }
// one run with multiple samples, so fix ID to just db name to ensure clean log name
ext.prefix = { "${meta.db_name}" }
publishDir = [
@ -457,6 +457,13 @@ process {
}
withName: MOTUS_PROFILE {
ext.args = {
[
params.motus_remove_ncbi_ids ? "" : "-p",
params.motus_use_relative_abundance ? "" : "-c",
params.motus_save_mgc_read_counts ? "-M ${task.ext.prefix}.mgc" : ""
].join(',').replaceAll(','," ")
}
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/motus/${meta.db_name}/" },

1
conf/test.config
View file

@ -52,6 +52,7 @@ params {
process {
withName: MALT_RUN {
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
}
withName: MEGAN_RMA2INFO_TSV {
maxForks = 1

3
conf/test_motus.config
View file

@ -44,5 +44,8 @@ params {
run_diamond = false
run_krakenuniq = false
run_motus = true
motus_save_mgc_read_counts = false
motus_remove_ncbi_ids = false
motus_use_relative_abundance = false
run_profile_standardisation = true
}

1
conf/test_nopreprocessing.config
View file

@ -46,5 +46,6 @@ params {
process {
withName: MALT_RUN {
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
}
}

1
conf/test_nothing.config
View file

@ -45,5 +45,6 @@ params {
process {
withName: MALT_RUN {
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
}
}

1
conf/test_pep.config
View file

@ -37,6 +37,7 @@ params {
process {
withName: MALT_RUN {
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
}
withName: MEGAN_RMA2INFO {
maxForks = 1

15
lib/WorkflowMain.groovy
View file

@ -12,9 +12,9 @@ class WorkflowMain {
// TODO nf-core: Add Zenodo DOI for pipeline after first release
//"* The pipeline\n" +
//" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
"* The nf-core framework\n" +
" https://doi.org/10.1038/s41587-020-0439-x\n\n" +
"* Software dependencies\n" +
'* The nf-core framework\n' +
' https://doi.org/10.1038/s41587-020-0439-x\n\n' +
'* Software dependencies\n' +
" https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
}
@ -53,15 +53,15 @@ class WorkflowMain {
System.exit(0)
}
// Print parameter summary log to screen
log.info paramsSummaryLog(workflow, params, log)
// Validate workflow parameters via the JSON schema
if (params.validate_params) {
NfcoreSchema.validateParameters(workflow, params, log)
}
// Print parameter summary log to screen
log.info paramsSummaryLog(workflow, params, log)
// Check that a -profile or Nextflow config has been provided to run the pipeline
NfcoreTemplate.checkConfigProvided(workflow, log)
@ -90,4 +90,5 @@ class WorkflowMain {
}
return null
}
}

2
modules.json
View file

@ -111,7 +111,7 @@
},
"malt/run": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "6d9712f03ec2de8264a50ee4541a617e1e063b51"
},
"megan/rma2info": {
"branch": "master",

8
modules/nf-core/malt/run/main.nf generated
View file

@ -2,14 +2,13 @@ process MALT_RUN {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::malt=0.41" : null)
conda (params.enable_conda ? "bioconda::malt=0.61" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/malt:0.41--1' :
'quay.io/biocontainers/malt:0.41--1' }"
'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' :
'quay.io/biocontainers/malt:0.61--hdfd78af_0' }"
input:
tuple val(meta), path(fastqs)
val mode
path index
output:
@ -38,7 +37,6 @@ process MALT_RUN {
-o . \\
$args \\
--inFile ${fastqs.join(' ')} \\
-m $mode \\
--index $index/ |&tee ${prefix}-malt-run.log
cat <<-END_VERSIONS > versions.yml

4
modules/nf-core/malt/run/meta.yml generated
View file

@ -28,10 +28,6 @@ input:
type: file
description: Input FASTQ files
pattern: "*.{fastq.gz,fq.gz}"
- mode:
type: string
description: Program mode
pattern: "Unknown|BlastN|BlastP|BlastX|Classifier"
- index:
type: directory
description: Index/database directory from malt-build

5
nextflow.config
View file

@ -145,7 +145,10 @@ params {
diamond_save_reads = false // this will override default diamond output format so no taxonomic profile is generated! added directly to module in profiling.nf
// mOTUs
run_motus = false
run_motus = false
motus_use_relative_abundance = false
motus_remove_ncbi_ids = false
motus_save_mgc_read_counts = false
// krona
run_krona = false

12
nextflow_schema.json
View file

@ -464,6 +464,18 @@
"type": "boolean",
"fa_icon": "fas fa-toggle-on",
"description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases"
},
"motus_use_relative_abundance": {
"type": "boolean",
"description": "Turn on printing relative abundance instead of counts."
},
"motus_save_mgc_read_counts": {
"type": "boolean",
"description": "Turn on saving the mgc reads count."
},
"motus_remove_ncbi_ids": {
"type": "boolean",
"description": "Turn on removing NCBI taxonomic IDs."
}
},
"fa_icon": "fas fa-align-center"

2
subworkflows/local/profiling.nf
View file

@ -97,7 +97,7 @@ workflow PROFILING {
db: it[2]
}
MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
MALT_RUN ( ch_input_for_malt.reads, ch_input_for_malt.db )
ch_maltrun_for_megan = MALT_RUN.out.rma6
.transpose()