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Minor update #20

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Merged
ypriverol merged 1 commit into from
Mar 30, 2026
Merged

Minor update #20

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4 changes: 2 additions & 2 deletions modules/local/diann/diann_msstats/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ process DIANN_MSSTATS {
label 'process_medium'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.25--pyh106432d_0' :
'biocontainers/quantms-utils:0.0.25--pyh106432d_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.27--pyh106432d_0' :
'biocontainers/quantms-utils:0.0.27--pyh106432d_0' }"

input:
path(report)
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4 changes: 2 additions & 2 deletions modules/local/diann/generate_cfg/main.nf
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Expand Up @@ -3,8 +3,8 @@ process GENERATE_CFG {
label 'process_tiny'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.25--pyh106432d_0' :
'biocontainers/quantms-utils:0.0.25--pyh106432d_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.27--pyh106432d_0' :
'biocontainers/quantms-utils:0.0.27--pyh106432d_0' }"

input:
val(meta)
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12 changes: 6 additions & 6 deletions modules/local/pmultiqc/main.nf
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Expand Up @@ -2,8 +2,8 @@ process PMULTIQC {
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pmultiqc:0.0.39--pyhdfd78af_0' :
'biocontainers/pmultiqc:0.0.39--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/pmultiqc:0.0.42--pyhdfd78af_0' :
'biocontainers/pmultiqc:0.0.42--pyhdfd78af_0' }"

input:
path 'results/*'
Expand All @@ -17,10 +17,10 @@ process PMULTIQC {

script:
def args = task.ext.args ?: ''
def disable_pmultiqc = (params.enable_pmultiqc) ? "--quantms_plugin" : ""
def disable_table_plots = (params.enable_pmultiqc) && (params.skip_table_plots) ? "--disable_table" : ""
def disable_idxml_index = (params.enable_pmultiqc) && (params.pmultiqc_idxml_skip) ? "--ignored_idxml" : ""
def contaminant_affix = params.contaminant_string ? "--contaminant_affix ${params.contaminant_string}" : ""
def disable_pmultiqc = (params.enable_pmultiqc) ? "--quantms-plugin" : ""
def disable_table_plots = (params.enable_pmultiqc) && (params.skip_table_plots) ? "--disable-table" : ""
def disable_idxml_index = (params.enable_pmultiqc) && (params.pmultiqc_idxml_skip) ? "--ignored-idxml" : ""
def contaminant_affix = params.contaminant_string ? "--contaminant-affix ${params.contaminant_string}" : ""

"""
set -x
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4 changes: 2 additions & 2 deletions modules/local/samplesheet_check/main.nf
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Expand Up @@ -4,8 +4,8 @@ process SAMPLESHEET_CHECK {
label 'process_tiny'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.25--pyh106432d_0' :
'biocontainers/quantms-utils:0.0.25--pyh106432d_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.27--pyh106432d_0' :
'biocontainers/quantms-utils:0.0.27--pyh106432d_0' }"

input:
path input_file
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4 changes: 2 additions & 2 deletions modules/local/sdrf_parsing/main.nf
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Expand Up @@ -3,8 +3,8 @@ process SDRF_PARSING {
label 'process_tiny'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.33--pyhdfd78af_0' :
'biocontainers/sdrf-pipelines:0.0.33--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.1.2--pyhdfd78af_0' :
'biocontainers/sdrf-pipelines:0.1.2--pyhdfd78af_0' }"

input:
path sdrf
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4 changes: 2 additions & 2 deletions modules/local/utils/mzml_statistics/main.nf
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Expand Up @@ -4,8 +4,8 @@ process MZML_STATISTICS {
label 'process_single'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.25--pyh106432d_0' :
'biocontainers/quantms-utils:0.0.25--pyh106432d_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.27--pyh106432d_0' :
'biocontainers/quantms-utils:0.0.27--pyh106432d_0' }"

input:
tuple val(meta), path(ms_file)
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1 change: 1 addition & 0 deletions workflows/dia.nf
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Expand Up @@ -159,6 +159,7 @@ workflow DIA {
emit:
versions = ch_software_versions
diann_report = diann_main_report
diann_log = FINAL_QUANTIFICATION.out.log
msstats_in = DIANN_MSSTATS.out.out_msstats
}

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1 change: 1 addition & 0 deletions workflows/quantmsdiann.nf
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Expand Up @@ -116,6 +116,7 @@ workflow QUANTMSDIANN {
ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_config)
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(FILE_PREPARATION.out.statistics)
ch_multiqc_files = ch_multiqc_files.mix(DIA.out.diann_log)
ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
ch_multiqc_quantms_logo = file("${projectDir}/assets/nf-core-quantmsdiann_logo_light.png")
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