Merge branch 'nf-core:master' into feature/bruker_data

nf-core · Jan 8, 2024 · 9612f9c · 9612f9c
2 parents 811eb96 + fa34d79
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.2.0dev] nfcore/quantms - [TBD] - Thimphu
+## [1.2.0] nfcore/quantms - [11/02/2023] - Thimphu
 
 ### `Added`
 
@@ -15,13 +15,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
-- Update for pmultiqc to pmultiqc=0.0.21
-- Update for openms to openms=3.1.0
+- [#314](https://github.com/bigbio/quantms/pull/314) Update for pmultiqc to pmultiqc=0.0.23
+- [#308](https://github.com/bigbio/quantms/pull/308) Update for openms to openms=3.1.0
 - Update for sdrf-pipelines to sdrf-pipelines=0.0.24
 - Update for msstats to msstats=4.2.1
 
 ### `Fixed`
 
+- [#316](https://github.com/bigbio/quantms/pull/316) Fixed jar path selection of luciphoradapter and msgf+
 - Fixed bug where modification masses were not calculated correctly in DIA-NN conversion.
 - Fixed multiple bugs Pull Request [#293 BigBio](https://github.com/bigbio/quantms/pull/293), [#279 BigBio](https://github.com/bigbio/quantms/pull/279), [#265 BigBio](https://github.com/bigbio/quantms/pull/265), [#260 BigBio](https://github.com/bigbio/quantms/pull/260), [#257 BigBio](https://github.com/bigbio/quantms/pull/257)
 
@@ -36,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - lfq_intensity_threshold: Minimum intensity of a feature to be considered in the MBR algorithm (default: 1000)
 - sage_processes: Number of processes to use in SAGE search engine (default: 1)
 - diann_speclib: Path to the spectral library to use in DIA-NN (default: null)
+- convert_dotd: if convert .d file to mzml (default: false)
 
 ### `Deprecations`
 

diff --git a/README.md b/README.md
@@ -3,12 +3,12 @@
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/quantms/results)[![Cite with Zenodo](https://img.shields.io/badge/DOI-10.5281/zenodo.7754148-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7754148)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
+[![run with conda](https://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/quantms)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23quantms-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/quantms)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+[![Get help on Slack](https://img.shields.io/badge/slack-nf--core%20%23quantms-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/quantms)[![Follow on Twitter](https://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](https://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 
@@ -33,7 +33,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 1. RAW file conversion to mzML ([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser))
 2. Peptide identification using [`comet`](https://uwpr.github.io/Comet/) and/or [`msgf+`](https://github.com/MSGFPlus/msgfplus)
 3. Re-scoring peptide identifications [`percolator`](https://github.com/percolator/percolator)
-4. Peptide identification FDR [`openms fdr tool`](https://github.com/ypriverol/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf)
+4. Peptide identification FDR [`openms fdr tool`](https://github.com/nf-core/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf)
 5. Modification localization [`luciphor`](https://github.com/dfermin/lucXor)
 6. Quantification: Feature detection [`proteomicsLFQ`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_ProteomicsLFQ.html)
 7. Protein inference and quantification [`proteomicsLFQ`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_ProteomicsLFQ.html)
@@ -45,7 +45,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 1. RAW file conversion to mzML ([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser))
 2. Peptide identification using [`comet`](https://uwpr.github.io/Comet/) and/or [`msgf+`](https://github.com/MSGFPlus/msgfplus)
 3. Re-scoring peptide identifications [`percolator`](https://github.com/percolator/percolator)
-4. Peptide identification FDR [`openms fdr tool`](https://github.com/ypriverol/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf)
+4. Peptide identification FDR [`openms fdr tool`](https://github.com/nf-core/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf)
 5. Modification localization [`luciphor`](https://github.com/dfermin/lucXor)
 6. Extracts and normalizes isobaric labeling [`IsobaricAnalyzer`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html)
 7. Protein inference [`ProteinInference`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteinInference.html) or [`Epifany`](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_Epifany.html) for bayesian inference.
@@ -55,10 +55,11 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ### DIA-LFQ (data-independent label-free quantification)
 
-1. RAW file conversion to mzML ([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser))
-2. DIA-NN analysis [`dia-nn`](https://github.com/vdemichev/DiaNN/)
-3. Generation of output files (msstats)
-4. QC reports generation [`pmultiqc`](https://github.com/bigbio/pmultiqc)
+1. RAW file conversion to mzML when RAW as input([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser))
+2. Performing an [optional step](https://github.com/nf-core/quantms/blob/dev/modules/local/tdf2mzml/main.nf): Converting .d to mzML when bruker data as input and set `convert_dotd` to true
+3. DIA-NN analysis [`dia-nn`](https://github.com/vdemichev/DiaNN/)
+4. Generation of output files (msstats)
+5. QC reports generation [`pmultiqc`](https://github.com/bigbio/pmultiqc)
 
 ### Functionality overview
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/quantms/releases/tag/dev" target="_blank">nf-core/quantms</a>
+  This report has been generated by the <a href="https://github.com/nf-core/quantms/releases/tag/1.2.0" target="_blank">nf-core/quantms</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/quantms/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/quantms/1.2.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   pmultiqc:
     order: 1

diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
@@ -44,28 +44,6 @@ def print_error(error, context="Line", context_str=""):
     sys.exit(1)
 
 
-def sniff_format(handle):
-    """
-    Detect the tabular format.
-
-    Args:
-        handle (text file): A handle to a `text file`_ object. The read position is
-        expected to be at the beginning (index 0).
-
-    Returns:
-        csv.Dialect: The detected tabular format.
-
-    .. _text file:
-        https://docs.python.org/3/glossary.html#term-text-file
-
-    """
-    peek = read_head(handle)
-    handle.seek(0)
-    sniffer = csv.Sniffer()
-    dialect = sniffer.sniff(peek)
-    return dialect
-
-
 def check_sdrf(check_ms, sdrf):
     df = SdrfDataFrame.parse(sdrf)
     errors = df.validate(DEFAULT_TEMPLATE)