From 88a2aba90dd38f1fa83157ec43f1017423fc0962 Mon Sep 17 00:00:00 2001 From: daichengxin <1278747277@qq.com> Date: Tue, 15 Mar 2022 13:00:08 +0800 Subject: [PATCH] update meta --- modules/local/convert2msstats/main.nf | 4 +- modules/local/convert2msstats/meta.yml | 50 +++++++--------------- modules/local/diann/meta.yml | 51 ++++++++++------------- modules/local/generate_diann_cfg/main.nf | 5 +-- modules/local/generate_diann_cfg/meta.yml | 51 +++++++++-------------- workflows/dia.nf | 2 +- 6 files changed, 62 insertions(+), 101 deletions(-) diff --git a/modules/local/convert2msstats/main.nf b/modules/local/convert2msstats/main.nf index 1acf593a..0929c9dd 100644 --- a/modules/local/convert2msstats/main.nf +++ b/modules/local/convert2msstats/main.nf @@ -1,9 +1,9 @@ process CONVERT2MSSTATS { label 'process_low' - conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) + conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.21" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/python:3.8.3" + container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.21--pyhdfd78af_0" } else { container "quay.io/biocontainers/sdrf-pipelines:0.0.21--pyhdfd78af_0" } diff --git a/modules/local/convert2msstats/meta.yml b/modules/local/convert2msstats/meta.yml index 9c8dfd96..1b11ad8d 100644 --- a/modules/local/convert2msstats/meta.yml +++ b/modules/local/convert2msstats/meta.yml @@ -1,45 +1,27 @@ -name: pmultiqc -description: A library for proteomics QC report based on MultiQC framework. +name: convert2msstats +description: A module to convert DIA report files to MSstats keywords: - - MultiQC - - QC - - Proteomics + - DIA-NN + - conversion + - MSstats tools: - - pmultiqc: + - custom: description: | - A library for proteomics QC report based on MultiQC framework. - homepage: https://github.com/bigbio/pmultiqc/ - documentation: https://github.com/bigbio/pmultiqc/ + A custom module for DIA-NN report file conversion. + homepage: https://github.com/bigbio/quantms + documentation: https://github.com/bigbio/quantms/tree/readthedocs input: - - expdesign: - type: file - description: experimental design file in openms style - - mzmls: - type: dir - description: mzML files directory - - quantms_results: - type: dir - description: the directory of quantms results including out.mzTab/out_msstats.csv - - raw_ids: - type: dir - description: idXML files directory -output: - report: type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - quantmsdb: + description: DIA-NN main report file + - exp_design: type: file - description: Sqlite3 database file stored protein psm and quantificaiton information - pattern: "*.db" - - data: - type: dir - description: MultiQC data dir - pattern: "multiqc_data" - - plots: + description: An experimental design file including Sample and replicates column et al. +output: + - out_msstats: type: file - description: Plots created by MultiQC - pattern: "*_data" + description: MSstats input file + pattern: "*.csv" - version: type: file description: File containing software version diff --git a/modules/local/diann/meta.yml b/modules/local/diann/meta.yml index 9c8dfd96..6854bcfd 100644 --- a/modules/local/diann/meta.yml +++ b/modules/local/diann/meta.yml @@ -1,45 +1,38 @@ -name: pmultiqc -description: A library for proteomics QC report based on MultiQC framework. +name: diann +description: A module for DIA library free analysis based on DIA-NN. keywords: - - MultiQC - - QC - - Proteomics + - DIA-NN + - library free + - DIA tools: - - pmultiqc: + - DIA-NN: description: | - A library for proteomics QC report based on MultiQC framework. - homepage: https://github.com/bigbio/pmultiqc/ - documentation: https://github.com/bigbio/pmultiqc/ + DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing by Demichev. + homepage: https://github.com/vdemichev/DiaNN + documentation: https://github.com/vdemichev/DiaNN input: - - expdesign: + - fasta: type: file - description: experimental design file in openms style - - mzmls: + description: FASTA sequence databases + - mzMLs: type: dir description: mzML files directory - - quantms_results: + - cfg: type: dir - description: the directory of quantms results including out.mzTab/out_msstats.csv - - raw_ids: - type: dir - description: idXML files directory + description: specifies a file to load options/commands from. output: - report: type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - quantmsdb: + description: Main report file,a text table containing precursor and protein IDs, as well as plenty of associated information. Most column names are self-explanatory. + pattern: "report.tsv" + - report_stat: type: file - description: Sqlite3 database file stored protein psm and quantificaiton information - pattern: "*.db" - - data: - type: dir - description: MultiQC data dir - pattern: "multiqc_data" - - plots: + description: Contains a number of QC metrics which can be used for data filtering, e.g. to exclude failed runs, or as a readout for method optimization. + pattern: "report.stats.tsv" + - log: type: file - description: Plots created by MultiQC - pattern: "*_data" + description: DIA-NN log file + pattern: "report.log.txt" - version: type: file description: File containing software version diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf index 8627c47b..739f3416 100644 --- a/modules/local/generate_diann_cfg/main.nf +++ b/modules/local/generate_diann_cfg/main.nf @@ -3,9 +3,9 @@ process GENERATE_DIANN_CFG { //TODO What images include click or use sys.args rather than click - conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) + conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.21" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/python:3.8.3" + container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.21--pyhdfd78af_0" } else { container "quay.io/biocontainers/sdrf-pipelines:0.0.21--pyhdfd78af_0" } @@ -13,7 +13,6 @@ process GENERATE_DIANN_CFG { input: val(meta) path(mzmls) - path(exp_design) output: path("*.mzML"), includeInputs: true, emit: mzmls_for_diann diff --git a/modules/local/generate_diann_cfg/meta.yml b/modules/local/generate_diann_cfg/meta.yml index 9c8dfd96..93f5ca8b 100644 --- a/modules/local/generate_diann_cfg/meta.yml +++ b/modules/local/generate_diann_cfg/meta.yml @@ -1,45 +1,32 @@ -name: pmultiqc -description: A library for proteomics QC report based on MultiQC framework. +name: generate_diann_cfg +description: A module to generate DIA-NN configure file. keywords: - - MultiQC - - QC - - Proteomics + - configure + - DIA-NN tools: - - pmultiqc: + - custom: description: | - A library for proteomics QC report based on MultiQC framework. - homepage: https://github.com/bigbio/pmultiqc/ - documentation: https://github.com/bigbio/pmultiqc/ + A custom module for DIA-NN configure file. + homepage: https://github.com/bigbio/quantms + documentation: https://github.com/bigbio/quantms/tree/readthedocs input: - - expdesign: - type: file - description: experimental design file in openms style + - meta: + type: map + description: Groovy Map containing sample information - mzmls: type: dir description: mzML files directory - - quantms_results: - type: dir - description: the directory of quantms results including out.mzTab/out_msstats.csv - - raw_ids: - type: dir - description: idXML files directory -output: - - report: + - exp_design: type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - quantmsdb: - type: file - description: Sqlite3 database file stored protein psm and quantificaiton information - pattern: "*.db" - - data: + description: An experimental design file including Sample and replicates column et al. +output: + - mzmls_for_diann: type: dir - description: MultiQC data dir - pattern: "multiqc_data" - - plots: + description: mzML files directory + - diann_cfg: type: file - description: Plots created by MultiQC - pattern: "*_data" + description: DIA-NN configure file + pattern: "*.cfg" - version: type: file description: File containing software version diff --git a/workflows/dia.nf b/workflows/dia.nf index 63c4b627..da561e9a 100644 --- a/workflows/dia.nf +++ b/workflows/dia.nf @@ -40,7 +40,7 @@ workflow DIA { } .set { result } - DIANNCFG(result.meta.collect(), result.mzml.collect(), ch_expdesign) + DIANNCFG(result.meta.collect(), result.mzml.collect()) ch_software_versions = ch_software_versions.mix(DIANNCFG.out.version.ifEmpty(null)) DIANN(DIANNCFG.out.mzmls_for_diann.collect(), Channel.fromPath(params.database), DIANNCFG.out.diann_cfg)