diff --git a/modules/local/openms/idfilter/main.nf b/modules/local/openms/idfilter/main.nf index 3def1ed5..d4763917 100644 --- a/modules/local/openms/idfilter/main.nf +++ b/modules/local/openms/idfilter/main.nf @@ -1,5 +1,4 @@ process IDFILTER { - tag "$meta.id" label 'process_very_low' label 'process_single_thread' diff --git a/modules/local/pmultiqc/main.nf b/modules/local/pmultiqc/main.nf index 025bbb51..35d2fd00 100644 --- a/modules/local/pmultiqc/main.nf +++ b/modules/local/pmultiqc/main.nf @@ -3,34 +3,32 @@ process PMULTIQC { conda (params.enable_conda ? "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.10" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.10--pyhdfd78af_0" + container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.11--pyhdfd78af_0" } else { - container "quay.io/biocontainers/pmultiqc:0.0.10--pyhdfd78af_0" + container "quay.io/biocontainers/pmultiqc:0.0.11--pyhdfd78af_0" } input: - path expdesign - path 'mzMLs/*' path 'results/*' - path 'raw_ids/*' path quantms_log output: path "*.html", emit: ch_pmultiqc_report - path "*.db", emit: ch_pmultiqc_db + path "*.db", optional:true, emit: ch_pmultiqc_db path "versions.yml", emit: versions path "*_data", emit: data path "*_plots", optional:true, emit: plots script: def args = task.ext.args ?: '' + def disable_pmultqic = params.enable_pmultiqc ? "": "--disable_plugin" """ multiqc \\ - --exp_design ${expdesign} \\ - --mzMLs ./mzMLs \\ - --raw_ids ./raw_ids \\ + -f \\ --config ./results/multiqc_config.yml \\ + ${args} \\ + ${disable_pmultqic} \\ ./results \\ -o . diff --git a/workflows/quantms.nf b/workflows/quantms.nf index a70055cf..2493ddbf 100644 --- a/workflows/quantms.nf +++ b/workflows/quantms.nf @@ -127,9 +127,7 @@ workflow QUANTMS { ch_versions = ch_versions.mix(LFQ.out.versions.ifEmpty(null)) DIA(ch_fileprep_result.dia, CREATE_INPUT_CHANNEL.out.ch_expdesign) - - // ch_ids_pmultiqc = ch_ids_pmultiqc.mix(DIA.out.ch_pmultiqc_ids) - // ch_pipeline_results = ch_pipeline_results.mix(DIA.out.final_result) + ch_pipeline_results = ch_pipeline_results.mix(DIA.out.diann_report) ch_versions = ch_versions.mix(DIA.out.versions.ifEmpty(null)) @@ -154,10 +152,10 @@ workflow QUANTMS { ch_multiqc_quantms_logo = file("$projectDir/assets/nf-core-quantms_logo_light.png") SUMMARYPIPELINE ( - CREATE_INPUT_CHANNEL.out.ch_expdesign, - ch_pmultiqc_mzmls.collect(), - ch_pipeline_results.combine(ch_multiqc_files.collect()), - ch_ids_pmultiqc.collect(), + CREATE_INPUT_CHANNEL.out.ch_expdesign + .combine(ch_pipeline_results.combine(ch_multiqc_files.collect()) + .combine(ch_pmultiqc_mzmls.collect()) + .combine(ch_ids_pmultiqc.collect().ifEmpty([]))), ch_multiqc_quantms_logo ) multiqc_report = SUMMARYPIPELINE.out.ch_pmultiqc_report.toList()