diff --git a/README.md b/README.md
index 2a694fdf..010c3a90 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# ![nf-core/quantms](docs/images/nf-core/quantms_logo_light.png#gh-light-mode-only) ![nf-core/quantms](docs/images/nf-core/quantms_logo_dark.png#gh-dark-mode-only)
+# ![nf-core/quantms](docs/images/nf-core-quantms_logo_light.png#gh-light-mode-only) ![nf-core/quantms](docs/images/nf-core-quantms_logo_dark.png#gh-dark-mode-only)
 
 [![GitHub Actions CI Status](https://github.com/nf-core/quantms/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/quantms/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/quantms/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/quantms/actions?query=workflow%3A%22nf-core+linting%22)
@@ -77,7 +77,7 @@ DIA-LFQ:
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
    ```console
-   nextflow run nf-core/quantms -profile test,YOURPROFILE --input project.sdrf.tsv --database protein.fasta
+   nextflow run nf-core/quantms -profile test,YOURPROFILE --input project.sdrf.tsv --database protein.fasta --outdir <OUTDIR>
    ```
 
    Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
@@ -97,7 +97,7 @@ DIA-LFQ:
    <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
 
    ```console
-   nextflow run nf-core/quantms -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input project.sdrf.tsv --database database.fasta
+   nextflow run nf-core/quantms -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input project.sdrf.tsv --database database.fasta --outdir <OUTDIR>
    ```
 
 ## Documentation
diff --git a/conf/dev.config b/conf/dev.config
index 3a6df93d..ae790eb8 100644
--- a/conf/dev.config
+++ b/conf/dev.config
@@ -1,11 +1,15 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running with nightly dev containers
- * -------------------------------------------------
- * Only overwrites the container. See dev/ folder for building instructions.
- * Use as follows:
- *   nextflow run nf-core/quantms -profile dev,<docker/singularity>
- */
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running with nightly dev. containers (mainly for OpenMS)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Only overwrites the container. E.g. uses the OpenMS nightly executable and thirdparty
+    containers. TODO Currently does nothing, we need to set it up.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test,<docker/singularity> [--outdir <OUTDIR>]
+
+-------------------------------------------------------------------------------------------
+*/
 
 params {
     config_profile_name = 'Development profile'
diff --git a/conf/modules.config b/conf/modules.config
index 9e021ac0..ebcaaf58 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -160,8 +160,8 @@ process {
         ]
     }
 
-    // EPIFILTER
-    withName: 'NFCORE_QUANTMS:QUANTMS:TMT:.*:EPIFILTER' {
+    // IDFILTER on PROTEIN LEVEL
+    withName: 'NFCORE_QUANTMS:QUANTMS:TMT:PROTEININFERENCE:IDFILTER' {
         ext.args    = [
             "-score:prot \"$params.protein_level_fdr_cutoff\"",
             "-delete_unreferenced_peptide_hits",
@@ -175,27 +175,22 @@ process {
         ]
     }
 
-    //IDCONFLICTRESOLVER
-    withName: 'NFCORE_QUANTMS:QUANTMS:TMT:PROTEINQUANT:IDCONFLICTRESOLVER' {
-        ext.args    = "-debug $params.conflict_resolver_debug"
-    }
-
-    //PROTEINQUANTIFIER
+    // PROTEINQUANTIFIER
     withName: 'NFCORE_QUANTMS:QUANTMS:TMT:PROTEINQUANT:PROTEINQUANTIFIER' {
-        ext.args    = "-debug $params.proteinquant_debug"
+        ext.args    = "-debug 0"
     }
 
-    // MSstatsConverter
+    // MSSTATSCONVERTER
     withName: 'NFCORE_QUANTMS:QUANTMS:TMT:PROTEINQUANT:MSSTATSCONVERTER' {
-        ext.args    = "-debug $params.msstatsconverter_debug"
+        ext.args    = "-debug 0"
     }
 }
 
-if (params.protein_inference_bayesian) {
+if (params.protein_inference_method == "bayesian") {
     process {
         // EPIFANY
         withName: 'NFCORE_QUANTMS:QUANTMS:.*:EPIFANY' {
-            ext.args    = "-debug $params.protein_inference_debug"
+            ext.args    = "-keep_best_psm_only false -debug $params.protein_inference_debug"
             publishDir  = [
                 path: { "${params.outdir}/epifany" },
                 mode: params.publish_dir_mode,
@@ -221,16 +216,6 @@ if (params.protein_inference_bayesian) {
 
 process {
 
-    // INDEXPEPTIDES
-    withName: 'NFCORE_QUANTMS:QUANTMS:.*:INDEXPEPTIDES' {
-        publishDir  = [
-            path: { "${params.outdir}/indexpeptides" },
-            mode: params.publish_dir_mode,
-            pattern: '*.log',
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     // IDFILTER
     withName: 'NFCORE_QUANTMS:QUANTMS:.*:ID:PSMFDRCONTROL:IDFILTER' {
         ext.args    = "-score:pep \"$params.psm_pep_fdr_cutoff\""
@@ -244,7 +229,7 @@ process {
 
     // PROTEOMICSLFQ
     withName: 'NFCORE_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ' {
-        ext.args    = "-debug $params.inf_quant_debug"
+        ext.args    = "-debug $params.plfq_debug"
     }
 
     // DIA-NN
diff --git a/conf/test.config b/conf/test.config
index 10bcf963..6be93226 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -1,24 +1,26 @@
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests (ISO)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/quantms -profile test,<docker/singularity>
+        nextflow run nf-core/quantms -profile test,<docker/singularity> [--outdir <OUTDIR>]
 
-----------------------------------------------------------------------------------------
+-------------------------------------------------------------------------------------------
 */
 
 params {
-    config_profile_name        = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name        = 'Test profile DDA ISO'
+    config_profile_description = 'Minimal test dataset to check pipeline function of the isotopic labelling branch of the pipeline'
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus   = 2
     max_memory = '6.GB'
     max_time   = '6.h'
 
+    outdir = "./results_iso"
+
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv'
 
diff --git a/conf/test_dia.config b/conf/test_dia.config
index 3d84dd4b..8ab5b74b 100644
--- a/conf/test_dia.config
+++ b/conf/test_dia.config
@@ -1,20 +1,26 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/quantms -profile test,<docker/singularity/podman>
- */
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests (DIA)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple test.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test_dia,<docker/singularity> [--outdir <OUTDIR>]
+
+------------------------------------------------------------------------------------------------
+*/
 
 params {
-    config_profile_name = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name        = 'Test profile for DIA'
+    config_profile_description = 'Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.'
+
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = 6.GB
     max_time = 48.h
 
+    outdir = './results_dia'
+
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci/PXD026600/PXD026600.sdrf.tsv'
     database = 'ftp://massive.ucsd.edu/MSV000087597/sequence/REF_EColi_K12_UPS1_combined.fasta'
diff --git a/conf/test_full.config b/conf/test_full.config
index 813aec9d..54af6b23 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -5,14 +5,16 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf-core/quantms -profile test_full,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/quantms -profile test_full,<docker/singularity> [--outdir <OUTDIR>]
 
 ----------------------------------------------------------------------------------------
 */
 
 params {
-    config_profile_name        = 'Full test profile'
-    config_profile_description = 'Full test dataset to check pipeline function and sanity of results'
+    config_profile_name        = 'Full test profile DDA ISO'
+    config_profile_description = 'Full test dataset in isotopic labelling mode to check pipeline function and sanity of results'
+
+    outdir = "./results_iso_full"
 
     // Input data for full size test
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv'
diff --git a/conf/test_lfq.config b/conf/test_lfq.config
index b72061d1..41959ef2 100644
--- a/conf/test_lfq.config
+++ b/conf/test_lfq.config
@@ -1,20 +1,26 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/quantms -profile test,<docker/singularity/podman>
- */
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests (LFQ)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple test.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test_lfq,<docker/singularity> [--outdir <OUTDIR>]
+
+------------------------------------------------------------------------------------------------
+*/
 
 params {
-    config_profile_name = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name        = 'Test profile for DDA LFQ'
+    config_profile_description = 'Minimal test dataset to check pipeline function of the label-free quantification branch of the pipeline'
+
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = 6.GB
     max_time = 48.h
 
+    outdir = "./results_lfq"
+
     // Input data
     labelling_type = "label free sample"
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci/BSA/BSA_design_urls.tsv'
@@ -25,5 +31,5 @@ params {
     enable_qc = true
     add_triqler_output = true
     protein_level_fdr_cutoff = 1.0
-    acqusition_method = "dda"
+    acquisition_method = "dda"
 }
diff --git a/conf/test_localize.config b/conf/test_localize.config
index 8e9ae1e6..7a64e2d2 100644
--- a/conf/test_localize.config
+++ b/conf/test_localize.config
@@ -1,22 +1,26 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running tests with
- *  modification localization
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/quantms -profile test_localize,<docker/singularity/podman>
- */
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests (LFQ) with mod. localization
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple test.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test_localize,<docker/singularity> [--outdir <OUTDIR>]
+
+----------------------------------------------------------------------------------------------------
+*/
 
 params {
-    config_profile_name = 'Test phospho-localization profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function for phospho-localization, SDRF parsing and ConsensusID.'
+    config_profile_name        = 'Test PTM-localization profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function for PTM-localization, SDRF parsing and ConsensusID.'
 
     // Limit resources so that this can run on Travis
     max_cpus = 2
     max_memory = 6.GB
     max_time = 1.h
 
+    outdir = "./results_localize"
+
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/phospho/test_phospho.sdrf'
     database = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci_phospho/pools_crap_targetdecoy.fasta'
diff --git a/modules/local/diannsearch/main.nf b/modules/local/diannsearch/main.nf
index ef74281a..9f2412a4 100644
--- a/modules/local/diannsearch/main.nf
+++ b/modules/local/diannsearch/main.nf
@@ -12,9 +12,9 @@ process DIANNSEARCH {
     file(diann_config)
 
     output:
-    path "report.tsv", emit: report
-    path "report.stats.tsv", emit: report_stat
-    path "report.log.txt", emit: log
+    path "diann_report.tsv", emit: report
+    path "diann_report.stats.tsv", emit: report_stat
+    path "diann_report.log.txt", emit: log
     path "versions.yml", emit: version
     path "*.tsv"
 
@@ -51,13 +51,14 @@ process DIANNSEARCH {
             ${mbr} \\
             --reannotate \\
             ${normalize} \\
+            --out diann_report.tsv \\
             --verbose $params.diann_debug \\
             > diann.log
 
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        DIA-NN: 1.8.0
+        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
     END_VERSIONS
     """
 }
diff --git a/modules/local/diannsearch/meta.yml b/modules/local/diannsearch/meta.yml
index 09aa7f5f..8b1de484 100644
--- a/modules/local/diannsearch/meta.yml
+++ b/modules/local/diannsearch/meta.yml
@@ -30,15 +30,15 @@ output:
   - report:
       type: file
       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"
+      pattern: "diann_report.tsv"
   - report_stat:
       type: file
       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"
+      pattern: "diann_report.stats.tsv"
   - log:
       type: file
       description: DIA-NN log file
-      pattern: "report.log.txt"
+      pattern: "diann_report.log.txt"
   - version:
       type: file
       description: File containing software version
diff --git a/modules/local/librarygeneration/main.nf b/modules/local/librarygeneration/main.nf
index 277c40d4..893af701 100644
--- a/modules/local/librarygeneration/main.nf
+++ b/modules/local/librarygeneration/main.nf
@@ -51,7 +51,7 @@ process LIBRARYGENERATION {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        DIA-NN: 1.8.0
+        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
     END_VERSIONS
     """
 }
diff --git a/modules/local/librarygeneration/meta.yml b/modules/local/librarygeneration/meta.yml
index 0133e1a9..ee117c7c 100644
--- a/modules/local/librarygeneration/meta.yml
+++ b/modules/local/librarygeneration/meta.yml
@@ -45,4 +45,4 @@ output:
       description: File containing software version
       pattern: "*.{version.txt}"
 authors:
-  - "@Chengxin Dai"
+  - "@daichengxin"
diff --git a/modules/local/openms/consensusid/main.nf b/modules/local/openms/consensusid/main.nf
index 811b8235..752acb65 100644
--- a/modules/local/openms/consensusid/main.nf
+++ b/modules/local/openms/consensusid/main.nf
@@ -2,11 +2,12 @@ process CONSENSUSID {
     label 'process_medium'
     // TODO could be easily parallelized
     label 'process_single_thread'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(id_file), val(qval_score)
diff --git a/modules/local/openms/decoydatabase/main.nf b/modules/local/openms/decoydatabase/main.nf
index 990d7797..19dd393a 100644
--- a/modules/local/openms/decoydatabase/main.nf
+++ b/modules/local/openms/decoydatabase/main.nf
@@ -1,9 +1,11 @@
 process DECOYDATABASE {
     label 'process_very_low'
+    label 'openms'
+
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     path(db_for_decoy)
diff --git a/modules/local/openms/epifany/main.nf b/modules/local/openms/epifany/main.nf
index d0b4254c..98592664 100644
--- a/modules/local/openms/epifany/main.nf
+++ b/modules/local/openms/epifany/main.nf
@@ -1,11 +1,13 @@
 process EPIFANY {
     label 'process_medium'
-    publishDir "${params.outdir}",
+    label 'openms'
 
-    conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2=2020_04_03 bioconda::msgf_plus=2021.03.22 bioconda::openms=2.8.0 bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1 bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 bioconda::openms-thirdparty=2.8.0" : null)
+    publishDir "${params.outdir}"
+
+    conda (params.enable_conda ? "bioconda::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(consus_file)
@@ -17,23 +19,24 @@ process EPIFANY {
 
     script:
     def args = task.ext.args ?: ''
+    gg = params.protein_quant == 'shared_peptides' ? 'remove_proteins_wo_evidence' : 'none'
 
     """
     Epifany \\
         -in ${consus_file} \\
         -protein_fdr true \\
         -threads $task.cpus \\
-        $args \\
         -algorithm:keep_best_PSM_only $params.keep_best_PSM_only \\
         -algorithm:update_PSM_probabilities $params.update_PSM_probabilities \\
-        -greedy_group_resolution $params.greedy_group_resolution \\
+        -greedy_group_resolution $gg \\
         -algorithm:top_PSMs $params.top_PSMs \\
         -out ${consus_file.baseName}_epi.consensusXML \\
+        $args \\
         > ${consus_file.baseName}_inference.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        DecoyDatabase: \$(Epifany 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g')
+        Epifany: \$(Epifany 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g')
     END_VERSIONS
     """
 }
diff --git a/modules/local/openms/extractpsmfeatures/main.nf b/modules/local/openms/extractpsmfeatures/main.nf
index ff7cc954..3f6d3dc6 100644
--- a/modules/local/openms/extractpsmfeatures/main.nf
+++ b/modules/local/openms/extractpsmfeatures/main.nf
@@ -1,11 +1,12 @@
 process EXTRACTPSMFEATURES {
     label 'process_very_low'
     label 'process_single_thread'
+    label 'openms'
 
     conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2=2020_04_03 bioconda::msgf_plus=2021.03.22 bioconda::openms=2.8.0 bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1 bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 bioconda::openms-thirdparty=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(id_file)
diff --git a/modules/local/openms/falsediscoveryrate/main.nf b/modules/local/openms/falsediscoveryrate/main.nf
index 2c2f414b..43d53816 100644
--- a/modules/local/openms/falsediscoveryrate/main.nf
+++ b/modules/local/openms/falsediscoveryrate/main.nf
@@ -1,11 +1,12 @@
 process FALSEDISCOVERYRATE {
-    label 'process_very_low'
+    label 'process_low'
     label 'process_single_thread'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(id_file)
diff --git a/modules/local/openms/filemerge/main.nf b/modules/local/openms/filemerge/main.nf
index 11b78b15..99bbd1d2 100644
--- a/modules/local/openms/filemerge/main.nf
+++ b/modules/local/openms/filemerge/main.nf
@@ -1,11 +1,12 @@
 process FILEMERGE {
     label 'process_medium'
     label 'process_single_thread'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     file(id_map)
@@ -24,9 +25,9 @@ process FILEMERGE {
         -in_type consensusXML \\
         -annotate_file_origin \\
         -append_method 'append_cols' \\
-        -debug $params.filemerge_debug \\
         -threads $task.cpus \\
         -out ID_mapper_merge.consensusXML \\
+        $args \\
         > ID_mapper_merge.log
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/local/openms/idconflictresolver/main.nf b/modules/local/openms/idconflictresolver/main.nf
index b8527c47..6857104c 100644
--- a/modules/local/openms/idconflictresolver/main.nf
+++ b/modules/local/openms/idconflictresolver/main.nf
@@ -1,10 +1,11 @@
 process IDCONFLICTRESOLVER {
     label 'process_low'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     path consus_file
@@ -21,8 +22,8 @@ process IDCONFLICTRESOLVER {
     IDConflictResolver \\
         -in ${consus_file} \\
         -threads $task.cpus \\
-        $args \\
         -out ${consus_file.baseName}_resconf.consensusXML \\
+        $args \\
         > ${consus_file.baseName}_resconf.log
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/local/openms/idfilter/main.nf b/modules/local/openms/idfilter/main.nf
index 20057aef..d4763917 100644
--- a/modules/local/openms/idfilter/main.nf
+++ b/modules/local/openms/idfilter/main.nf
@@ -1,11 +1,13 @@
 process IDFILTER {
+
     label 'process_very_low'
     label 'process_single_thread'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(id_file)
@@ -25,7 +27,6 @@ process IDFILTER {
         -out ${id_file.baseName}_filter$suffix \\
         -threads $task.cpus \\
         $args \\
-        -debug $params.idfilter_debug \\
         > ${id_file.baseName}_idfilter.log
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/local/openms/idmapper/main.nf b/modules/local/openms/idmapper/main.nf
index 9c52cfbe..0d3ff125 100644
--- a/modules/local/openms/idmapper/main.nf
+++ b/modules/local/openms/idmapper/main.nf
@@ -1,11 +1,13 @@
 process IDMAPPER {
     tag "$meta.id"
+
     label 'process_medium'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(id_file), path(map_file)
@@ -24,8 +26,8 @@ process IDMAPPER {
         -id ${id_file} \\
         -in ${map_file} \\
         -threads $task.cpus \\
-        $args \\
         -out ${id_file.baseName}_map.consensusXML \\
+        $args \\
         > ${id_file.baseName}_map.log
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/local/openms/idpep/main.nf b/modules/local/openms/idpep/main.nf
index 1d4e1e9d..c6185288 100644
--- a/modules/local/openms/idpep/main.nf
+++ b/modules/local/openms/idpep/main.nf
@@ -3,8 +3,8 @@ process IDPEP {
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(id_file)
diff --git a/modules/local/openms/idscoreswitcher/main.nf b/modules/local/openms/idscoreswitcher/main.nf
index a258124c..a6644af5 100644
--- a/modules/local/openms/idscoreswitcher/main.nf
+++ b/modules/local/openms/idscoreswitcher/main.nf
@@ -5,8 +5,8 @@ process IDSCORESWITCHER {
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(id_file), val(new_score)
diff --git a/modules/local/openms/indexpeptides/main.nf b/modules/local/openms/indexpeptides/main.nf
index b80ac057..f733d838 100644
--- a/modules/local/openms/indexpeptides/main.nf
+++ b/modules/local/openms/indexpeptides/main.nf
@@ -3,8 +3,8 @@ process INDEXPEPTIDES {
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(id_file), path(database)
diff --git a/modules/local/openms/isobaricanalyzer/main.nf b/modules/local/openms/isobaricanalyzer/main.nf
index afeb9a2d..77599888 100644
--- a/modules/local/openms/isobaricanalyzer/main.nf
+++ b/modules/local/openms/isobaricanalyzer/main.nf
@@ -4,8 +4,8 @@ process ISOBARICANALYZER {
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(mzml_file)
@@ -38,8 +38,8 @@ process ISOBARICANALYZER {
         -extraction:precursor_isotope_deviation $params.precursor_isotope_deviation \\
         ${iso_normalization} \\
         -${meta.labelling_type}:reference_channel $params.reference_channel \\
-        $args \\
         -out ${mzml_file.baseName}_iso.consensusXML \\
+        $args \\
         > ${mzml_file.baseName}_isob.log
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/local/openms/msstatsconverter/main.nf b/modules/local/openms/msstatsconverter/main.nf
index 7950f7c3..59b17411 100644
--- a/modules/local/openms/msstatsconverter/main.nf
+++ b/modules/local/openms/msstatsconverter/main.nf
@@ -3,8 +3,8 @@ process MSSTATSCONVERTER {
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     path consensusXML
diff --git a/modules/local/openms/mzmlindexing/main.nf b/modules/local/openms/mzmlindexing/main.nf
index 196795ae..62fff846 100644
--- a/modules/local/openms/mzmlindexing/main.nf
+++ b/modules/local/openms/mzmlindexing/main.nf
@@ -4,8 +4,8 @@ process MZMLINDEXING {
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(mzmlfile)
diff --git a/modules/local/openms/openmspeakpicker/main.nf b/modules/local/openms/openmspeakpicker/main.nf
index ef2274c3..9346abfb 100644
--- a/modules/local/openms/openmspeakpicker/main.nf
+++ b/modules/local/openms/openmspeakpicker/main.nf
@@ -4,8 +4,8 @@ process OPENMSPEAKPICKER {
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(mzml_file)
diff --git a/modules/local/openms/proteininference/main.nf b/modules/local/openms/proteininference/main.nf
index bfcfb0da..1ed84361 100644
--- a/modules/local/openms/proteininference/main.nf
+++ b/modules/local/openms/proteininference/main.nf
@@ -3,8 +3,8 @@ process PROTEININFERENCE {
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(consus_file)
@@ -16,6 +16,8 @@ process PROTEININFERENCE {
 
     script:
     def args = task.ext.args ?: ''
+    gg = params.protein_quant == 'shared_peptides' ? '-Algorithm:greedy_group_resolution' : ''
+    groups = params.protein_quant == 'strictly_unique_peptides' ? 'false' : 'true'
 
     """
     ProteinInference \\
@@ -24,10 +26,13 @@ process PROTEININFERENCE {
         -picked_fdr $params.picked_fdr \\
         -picked_decoy_string $params.decoy_string \\
         -protein_fdr true \\
+        -Algorithm:use_shared_peptides $params.use_shared_peptides \\
+        -Algorithm:annotate_indistinguishable_groups $groups \\
+        $gg \\
         -Algorithm:score_aggregation_method $params.protein_score \\
-        $args \\
         -Algorithm:min_peptides_per_protein $params.min_peptides_per_protein \\
         -out ${consus_file.baseName}_epi.consensusXML \\
+        $args \\
         > ${consus_file.baseName}_inference.log
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/local/openms/proteinquantifier/main.nf b/modules/local/openms/proteinquantifier/main.nf
index d04ac553..49ab74c5 100644
--- a/modules/local/openms/proteinquantifier/main.nf
+++ b/modules/local/openms/proteinquantifier/main.nf
@@ -3,8 +3,8 @@ process PROTEINQUANTIFIER {
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     path epi_filt_resolve
diff --git a/modules/local/openms/proteomicslfq/main.nf b/modules/local/openms/proteomicslfq/main.nf
index a2151166..1aff7dca 100644
--- a/modules/local/openms/proteomicslfq/main.nf
+++ b/modules/local/openms/proteomicslfq/main.nf
@@ -3,8 +3,8 @@ process PROTEOMICSLFQ {
 
     conda (params.enable_conda ? "openms::openms=2.8.0.dev" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     path(mzmls)
@@ -15,7 +15,7 @@ process PROTEOMICSLFQ {
     output:
     path "out.mzTab", emit: out_mztab
     path "out.consensusXML", emit: out_consensusXML
-    path "out_msstats.csv", emit: out_msstats
+    path "out_msstats.csv", emit: out_msstats optional true
     path "out_triqler.tsv", emit: out_triqler optional true
     path "debug_mergedIDs.idXML", emit: debug_mergedIDs optional true
     path "debug_mergedIDs_inference.idXML", emit: debug_mergedIDs_inference optional true
diff --git a/modules/local/openms/thirdparty/searchenginecomet/main.nf b/modules/local/openms/thirdparty/searchenginecomet/main.nf
index 1fa53461..9eb86a1a 100644
--- a/modules/local/openms/thirdparty/searchenginecomet/main.nf
+++ b/modules/local/openms/thirdparty/searchenginecomet/main.nf
@@ -2,7 +2,7 @@ process SEARCHENGINECOMET {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2=2020_04_03 bioconda::msgf_plus=2021.03.22 bioconda::openms=2.8.0 bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1 bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 bioconda::openms-thirdparty=2.8.0" : null)
+    conda (params.enable_conda ? "bioconda::openms-thirdparty=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
         'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
@@ -67,6 +67,18 @@ process SEARCHENGINECOMET {
         else if (meta.enzyme == "Lys-C") enzyme = "Lys-C/P"
     }
 
+    num_enzyme_termini = ""
+    if (meta.enzyme == "unspecific cleavage")
+    {
+        num_enzyme_termini = "none"
+    }
+    else if (params.num_enzyme_termini == "fully")
+    {
+        num_enzyme_termini = "full"
+    }
+
+    il_equiv = params.IL_equivalent ? "-PeptideIndexing:IL_equivalent" : ""
+
     """
     CometAdapter \\
         -in ${mzml_file} \\
@@ -89,6 +101,8 @@ process SEARCHENGINECOMET {
         -precursor_error_units $meta.precursormasstoleranceunit \\
         -fragment_mass_tolerance ${bin_tol} \\
         -fragment_bin_offset ${bin_offset} \\
+        ${il_equiv} \\
+        -PeptideIndexing:unmatched_action ${params.unmatched_action} \\
         -debug $params.db_debug \\
         -force \\
         $args \\
diff --git a/modules/local/openms/thirdparty/searchenginemsgf/main.nf b/modules/local/openms/thirdparty/searchenginemsgf/main.nf
index 73ca0d10..07eb51e0 100644
--- a/modules/local/openms/thirdparty/searchenginemsgf/main.nf
+++ b/modules/local/openms/thirdparty/searchenginemsgf/main.nf
@@ -2,7 +2,7 @@ process SEARCHENGINEMSGF {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2=2020_04_03 bioconda::msgf_plus=2021.03.22 bioconda::openms=2.8.0 bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1 bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 bioconda::openms-thirdparty=2.8.0" : null)
+    conda (params.enable_conda ? "bioconda::openms-thirdparty=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
         'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
@@ -45,6 +45,18 @@ process SEARCHENGINEMSGF {
         inst = params.instrument ?: "low_res"
     }
 
+    num_enzyme_termini = ""
+    if (meta.enzyme == "unspecific cleavage")
+    {
+        num_enzyme_termini = "none"
+    }
+    else if (params.num_enzyme_termini == "fully")
+    {
+        num_enzyme_termini = "full"
+    }
+
+    il_equiv = params.IL_equivalent ? "-PeptideIndexing:IL_equivalent" : ""
+
     """
     MSGFPlusAdapter \\
         -protocol $params.protocol \\
@@ -68,6 +80,8 @@ process SEARCHENGINEMSGF {
         -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect() { "'${it}'" }.join(" ") } \\
         -variable_modifications ${meta.variablemodifications.tokenize(',').collect() { "'${it}'" }.join(" ") } \\
         -max_mods $params.max_mods \\
+        ${il_equiv} \\
+        -PeptideIndexing:unmatched_action ${params.unmatched_action} \\
         -debug $params.db_debug \\
         $args \\
         > ${mzml_file.baseName}_msgf.log
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/nextflow.config b/nextflow.config
index 3a1fba9d..b2dea632 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,88 +10,85 @@
 params {
 
     // Workflow flags
-    input = null // the sdrf and spectra parameters are inferred from this one
-    root_folder = null
-    local_input_type = null
-    database = null
-    acqusition_method = null
+    input              = null // the sdrf and spectra parameters are inferred from this one
+    root_folder        = null
+    local_input_type   = null
+    database           = null
+    acquisition_method = null
 
     // Tools flags
-    posterior_probabilities = 'percolator'
-    add_decoys = false
-    enable_pmultiqc = true
-    search_engines = 'comet'
-    psm_pep_fdr_cutoff = 0.10
+    posterior_probabilities  = 'percolator'
+    add_decoys               = false
+    enable_pmultiqc          = true
+    search_engines           = 'comet'
+    psm_pep_fdr_cutoff       = 0.10
     protein_level_fdr_cutoff = 0.05
 
     // Debug level
-    decoydatabase_debug = 0
-    pp_debug = 0
-    idfilter_debug = 0
-    idscoreswitcher_debug = 0
-    iso_debug = 0
-    db_debug = 0
-    idpep_debug = 0
-    percolator_debug = 0
-    consensusid_debug = 0
-    idmapper_debug = 0
-    filemerge_debug = 0
-    conflict_resolver_debug = 0
-    luciphor_debug = 0
+    decoydatabase_debug     = 0
+    pp_debug                = 0
+    idfilter_debug          = 0
+    idscoreswitcher_debug   = 0
+    iso_debug               = 0
+    db_debug                = 0
+    idpep_debug             = 0
+    percolator_debug        = 0
+    consensusid_debug       = 0
+    idmapper_debug          = 0
+    luciphor_debug          = 0
     protein_inference_debug = 0
-    proteinquant_debug = 0
-    inf_quant_debug = 0
+    plfq_debug              = 0
 
     // decoys
-    decoy_string = 'DECOY_'
-    decoy_string_position = 'prefix'
-    decoy_method = 'reverse'
-    shuffle_max_attempts = 30
+    decoy_string                        = 'DECOY_'
+    decoy_string_position               = 'prefix'
+    decoy_method                        = 'reverse'
+    shuffle_max_attempts                = 30
     shuffle_sequence_identity_threshold = 0.5
 
     // peak picking if used
-    openms_peakpicking = false
-    peakpicking_inmemory = false
+    openms_peakpicking    = false
+    peakpicking_inmemory  = false
     peakpicking_ms_levels = null // means all/auto
 
     //Isobaric analyze
-    labelling_type = null
-    reference_channel = 126
-    min_precursor_intensity = 1.0
-    reporter_mass_shift = 0.002
-    select_activation = 'HCD'
-    isotope_correction = true
-    iso_normalization = false
-    min_reporter_intensity = 0.0
-    min_precursor_purity = 0.0
+    labelling_type              = null
+    reference_channel           = 126
+    min_precursor_intensity     = 1.0
+    reporter_mass_shift         = 0.002
+    select_activation           = 'HCD'
+    isotope_correction          = true
+    iso_normalization           = false
+    min_reporter_intensity      = 0.0
+    min_precursor_purity        = 0.0
     precursor_isotope_deviation = 10.0
 
     // shared search engine parameters
-    enzyme = 'Trypsin'
-    num_enzyme_termini = 'fully'
-    allowed_missed_cleavages = 2
-    precursor_mass_tolerance = 5
+    enzyme                        = 'Trypsin'
+    num_enzyme_termini            = 'fully'
+    allowed_missed_cleavages      = 2
+    precursor_mass_tolerance      = 5
     precursor_mass_tolerance_unit = 'ppm'
-    fixed_mods = 'Carbamidomethyl (C)'
-    variable_mods = 'Oxidation (M)'
-    enable_mod_localization = false
-    mod_localization = 'Phospho (S),Phospho (T),Phospho (Y)'
-    fragment_mass_tolerance = 0.03
-    fragment_mass_tolerance_unit = 'Da'
-    fragment_method = 'HCD' //currently unused. hard to find a good logic to beat the defaults
-    isotope_error_range = '0,1'
-    instrument = null //auto-determined from tolerances
-    protocol = 'automatic'
-    min_precursor_charge = 2
-    max_precursor_charge = 4
-    min_peptide_length = 6
-    max_peptide_length = 40
-    num_hits = 1
-    max_mods = 3
+    fixed_mods                    = 'Carbamidomethyl (C)'
+    variable_mods                 = 'Oxidation (M)'
+    enable_mod_localization       = false
+    mod_localization              = 'Phospho (S),Phospho (T),Phospho (Y)'
+    fragment_mass_tolerance       = 0.03
+    fragment_mass_tolerance_unit  = 'Da'
+    fragment_method               = 'HCD' //currently unused. hard to find a good logic to beat the defaults
+    isotope_error_range           = '0,1'
+    instrument                    = null //auto-determined from tolerances
+    protocol                      = 'automatic'
+    min_precursor_charge          = 2
+    max_precursor_charge          = 4
+    min_peptide_length            = 6
+    max_peptide_length            = 40
+    num_hits                      = 1
+    max_mods                      = 3
 
     // PeptideIndexer flags
-    IL_equivalent = true
-    allow_unmatched = false
+    IL_equivalent    = true
+    unmatched_action = "warn"
 
     // IDPEP flags
     outlier_handling = "none"
@@ -100,72 +97,70 @@ params {
     protein = false
 
     // Percolator flags
-    train_FDR = 0.05
-    test_FDR = 0.05
-    FDR_level = 'peptide-level-fdrs'
-    klammer = false
+    train_FDR                    = 0.05
+    test_FDR                     = 0.05
+    FDR_level                    = 'peptide-level-fdrs'
+    klammer                      = false
     description_correct_features = 0
-    subset_max_train = 300000
+    subset_max_train             = 300000
 
     // ConsensusID
-    consensusid_algorithm = 'best'
-    min_consensus_support = 0
+    consensusid_algorithm           = 'best'
+    min_consensus_support           = 0
     consensusid_considered_top_hits = 0
 
     // Luciphor options
-    luciphor_neutral_losses = null
-    luciphor_decoy_mass = null
+    luciphor_neutral_losses       = null
+    luciphor_decoy_mass           = null
     luciphor_decoy_neutral_losses = null
 
     // Epifany
-    protein_inference_bayesian = false
-    greedy_group_resolution = 'none'
-    top_PSMs = 1
-    update_PSM_probabilities = true
-    keep_best_PSM_only = true
+    top_PSMs                 = 1
+    update_PSM_probabilities = false
 
     // Protein inference
-    picked_fdr = true
-    protein_score = 'best' // Other options are "Best", "Product", "Sum"
+    picked_fdr               = true
+    protein_score            = 'best' // Other options are "Best", "Product", "Sum"
     min_peptides_per_protein = 1
+    use_shared_peptides      = true
 
     // ProteinQuantifier
-    top = 3
-    average = 'median'
+    top                      = 3
+    average                  = 'median'
     best_charge_and_fraction = false
-    normalize = false
-    ratios = false
-    fix_peptides = false
-    include_all = true
+    normalize                = false
+    ratios                   = false
+    fix_peptides             = false
+    include_all              = true
 
     // ProteomicsLFQ flags
     protein_inference_method = 'aggregation'
-    protein_quant = 'unique_peptides'
-    quantification_method = 'feature_intensity'
-    targeted_only = true
-    mass_recalibration = false
-    transfer_ids = 'false'
-    alignment_order = 'star'
-    add_triqler_output = false
-    quantify_decoys = false
+    protein_quant            = 'unique_peptides'
+    quantification_method    = 'feature_intensity'
+    targeted_only            = true
+    mass_recalibration       = false
+    transfer_ids             = 'false'
+    alignment_order          = 'star'
+    add_triqler_output       = false
+    quantify_decoys          = false
 
     // DIA-NN
-    matrix_spec_q = 0.01
-    diann_debug = 3
-    min_pr_mz = null
-    max_pr_mz = null
-    min_fr_mz = null
-    max_fr_mz = null
+    matrix_spec_q   = 0.01
+    diann_debug     = 3
+    // TODO think about unifying it with DDA parameters
+    min_pr_mz       = null
+    max_pr_mz       = null
+    min_fr_mz       = null
+    max_fr_mz       = null
     diann_normalize = true
 
     // MSstats
-    msstatsconverter_debug = 0
     skip_post_msstats = false
-    ref_condition = null
-    contrasts = 'pairwise'
+    ref_condition     = null
+    contrasts         = 'pairwise'
 
     // PTXQC
-    enable_qc = false
+    enable_qc           = false
     ptxqc_report_layout = null
 
     // MultiQC options
@@ -174,7 +169,7 @@ params {
     max_multiqc_email_size     = '25.MB'
 
     // Boilerplate options
-    outdir                     = './results'
+    outdir                     = null
     publish_dir_mode           = 'copy'
     tracedir                   = "${params.outdir}/pipeline_info"
     email                      = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index b035553d..c5f081dc 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -14,8 +14,8 @@
             "properties": {
                 "input": {
                     "type": "string",
-                    "description": "URI/path to an [SDRF](https://github.com/bigbio/proteomics-metadata-standard/tree/master/annotated-projects) file **OR** globbing pattern for URIs/paths of mzML or Thermo RAW files",
-                    "help_text": "The input to the pipeline can be specified in two **mutually exclusive** ways:\n  - using a path or URI to a PRIDE Sample to Data Relation Format file (SDRF), e.g. as part of a submitted and\nannotated PRIDE experiment (see [here](https://github.com/bigbio/proteomics-metadata-standard/tree/master/annotated-projects) for examples). Input files will be downloaded and cached from the URIs specified in the SDRF file.\nAn OpenMS-style experimental design will be generated based on the factor columns of the SDRF. The settings for the\nfollowing parameters will currently be overwritten by the ones specified in the SDRF:\n\n    * `fixed_mods`,\n    * `variable_mods`,\n    * `precursor_mass_tolerance`,\n    * `precursor_mass_tolerance_unit`,\n    * `fragment_mass_tolerance`,\n    * `fragment_mass_tolerance_unit`,\n    * `fragment_method`,\n    * `enzyme`\n  - by specifying globbing patterns to the input spectrum files in Thermo RAW or mzML format (e.g. `/data/experiment{1,2,3}_rep*.mzML`). An experimental design should be provided with the `expdesign` parameter.",
+                    "description": "URI/path to an [SDRF](https://github.com/bigbio/proteomics-metadata-standard/tree/master/annotated-projects) file (.sdrf.tsv) **OR** [OpenMS-style experimental design](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html#details) with paths to spectra files (.tsv)",
+                    "help_text": "Input is specified by using a path or URI to a PRIDE Sample to Data Relation Format file (SDRF), e.g. as part of a submitted and\nannotated PRIDE experiment (see [here](https://github.com/bigbio/proteomics-metadata-standard/tree/master/annotated-projects) for examples). Input files will be downloaded and cached from the URIs specified in the SDRF file.\nAn OpenMS-style experimental design will be generated based on the factor columns of the SDRF. The settings for the\nfollowing parameters will currently be overwritten by the ones specified in the SDRF:\n\n    * `fixed_mods`,\n    * `variable_mods`,\n    * `precursor_mass_tolerance`,\n    * `precursor_mass_tolerance_unit`,\n    * `fragment_mass_tolerance`,\n    * `fragment_mass_tolerance_unit`,\n    * `fragment_method`,\n    * `enzyme`\n  You can also specify an [OpenMS-style experimental design](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html#details) directly (.tsv ending). In this case, the aforementioned parameters have to be specified or defaults will be used.",
                     "fa_icon": "fas fa-file-csv"
                 },
                 "outdir": {
@@ -35,29 +35,20 @@
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
-                }
-            }
-        },
-        "main_parameters_sdrf": {
-            "title": "Main parameters (SDRF)",
-            "type": "object",
-            "description": "In case your input was an SDRF files, the following optional parameters can be set.",
-            "default": "",
-            "properties": {
+                },
                 "root_folder": {
                     "type": "string",
-                    "description": "Root folder in which the spectrum files specified in the SDRF are searched",
+                    "description": "Root folder in which the spectrum files specified in the SDRF/design are searched",
                     "fa_icon": "fas fa-folder",
-                    "help_text": "This optional parameter can be used to specify a root folder in which the spectrum files specified in the SDRF are searched.\nIt is usually used if you have a local version of the experiment already. Note that this option does not support recursive\nsearching yet."
+                    "help_text": "This optional parameter can be used to specify a root folder in which the spectrum files specified in the SDRF/design are searched.\nIt is usually used if you have a local version of the experiment already. Note that this option does not support recursive\nsearching yet."
                 },
                 "local_input_type": {
                     "type": "string",
-                    "description": "Overwrite the file type/extension of the filename as specified in the SDRF",
+                    "description": "Overwrite the file type/extension of the filename as specified in the SDRF/design",
                     "fa_icon": "fas fa-file-invoice",
-                    "help_text": "If the above [`--root_folder`](#params_root_folder) was given to load local input files, this overwrites the file type/extension of\nthe filename as specified in the SDRF. Usually used in case you have an mzML-converted version of the files already. Needs to be\none of 'mzML' or 'raw' (the letter cases should match your files exactly)."
+                    "help_text": "If the above [`--root_folder`](#params_root_folder) was given to load local input files, this overwrites the file type/extension of\nthe filename as specified in the SDRF/design. Usually used in case you have an mzML-converted version of the files already. Needs to be\none of 'mzML' or 'raw' (the letter cases should match your files exactly)."
                 }
-            },
-            "fa_icon": "far fa-chart-bar"
+            }
         },
         "protein_database": {
             "title": "Protein database",
@@ -148,98 +139,6 @@
             },
             "fa_icon": "far fa-chart-bar"
         },
-        "isobaric_analyzer": {
-            "title": "Isobaric analyzer",
-            "type": "object",
-            "description": "Extracts and normalizes labeling information",
-            "default": "",
-            "properties": {
-                "labelling_type": {
-                    "type": "string",
-                    "description": "label method",
-                    "fa_icon": "fas fa-font",
-                    "help_text": "Isobaric Quantification method used in the experiment",
-                    "enum": [
-                        "label free sample",
-                        "itraq4plex",
-                        "itraq8plex",
-                        "tmt6plex",
-                        "tmt10plex",
-                        "tmt11plex",
-                        "tmt16plex"
-                    ]
-                },
-                "select_activation": {
-                    "type": "string",
-                    "description": "Operate only on MSn scans where any of its precursors features a certain activation method.",
-                    "fa_icon": "fas fa-font",
-                    "help_text": "Operate only on MSn scans where any of its precursors features a certain activation method. Set to empty to disable",
-                    "enum": ["HCD", "CID", "ETD", "ECD"]
-                },
-                "reporter_mass_shift": {
-                    "type": "number",
-                    "description": "Allowed shift (left to right) in Th from the expected position",
-                    "default": 0.002,
-                    "fa_icon": "fas fa-sliders-h",
-                    "help_text": "Allowed shift (left to right) in Th from the expected position."
-                },
-                "min_precursor_intensity": {
-                    "type": "number",
-                    "description": "Minimum intensity of the precursor to be extracted",
-                    "default": 1.0,
-                    "fa_icon": "fas fa-sliders-h"
-                },
-                "min_precursor_purity": {
-                    "type": "number",
-                    "description": "Minimum fraction of the total intensity. 0.0:1.0",
-                    "default": 0.0,
-                    "fa_icon": "fas fa-sliders-h",
-                    "help_text": "Minimum fraction of the total intensity in the isolation window of the precursor spectrum"
-                },
-                "min_reporter_intensity": {
-                    "type": "number",
-                    "description": "Minimum intensity of the individual reporter ions to be extracted.",
-                    "default": 0.0,
-                    "fa_icon": "fas fa-sliders-h",
-                    "help_text": "Minimum intensity of the individual reporter ions to be extracted."
-                },
-                "precursor_isotope_deviation": {
-                    "type": "number",
-                    "description": "Maximum allowed deviation (in ppm) betweed theoretical and observed isotopic peaks of the precursor peak",
-                    "default": 10.0,
-                    "fa_icon": "fas fa-sliders-h",
-                    "help_text": "Maximum allowed deviation (in ppm) betweed theoretical and observed isotopic peaks of the precursor peak."
-                },
-                "isotope_correction": {
-                    "type": "boolean",
-                    "description": "Enable isotope correction (highly recommended)",
-                    "default": true,
-                    "fa_icon": "fas fa-toggle-on"
-                },
-                "iso_normalization": {
-                    "type": "boolean",
-                    "description": "Enable normalization of the channel intensities",
-                    "default": false,
-                    "fa_icon": "fas fa-toggle-on",
-                    "help_text": "The normalization is done by using the Median of Rations.Also the ratios the medians is provided as control measure."
-                },
-                "reference_channel": {
-                    "type": "integer",
-                    "description": "The reference channel",
-                    "fa_icon": "fas fa-list-ol",
-                    "help_text": "The reference channel",
-                    "default": 126
-                },
-                "iso_debug": {
-                    "type": "integer",
-                    "description": "set the debug level",
-                    "fa_icon": "fas fa-bug",
-                    "default": 0,
-                    "hidden": true
-                }
-            },
-            "fa_icon": "far fa-chart-bar"
-        },
         "database_search": {
             "title": "Database search",
             "type": "object",
@@ -440,19 +339,18 @@
             "description": "",
             "default": "",
             "properties": {
-                "allow_unmatched": {
-                    "type": "boolean",
-                    "description": "Do not fail if there are some unmatched peptides. Only activate as last resort, if you know that the rest of your settings are fine!",
-                    "default": false,
+                "unmatched_action": {
+                    "type": "string",
+                    "description": "What to do when peptides are found that do not follow a unified set of rules (since search engines sometimes differ in their interpretation of them). ",
+                    "default": "warn",
                     "fa_icon": "far fa-check-square",
-                    "enum": [false, true]
+                    "enum": ["warn", "error", "remove"]
                 },
                 "IL_equivalent": {
                     "type": "boolean",
                     "description": "Should isoleucine and leucine be treated interchangeably when mapping search engine hits to the database? Default: true",
                     "default": true,
-                    "fa_icon": "far fa-check-square",
-                    "enum": [true, false]
+                    "fa_icon": "far fa-check-square"
                 }
             },
             "fa_icon": "fas fa-project-diagram"
@@ -633,48 +531,46 @@
                 }
             }
         },
-        "file_merge": {
-            "title": "File Merge",
-            "type": "object",
-            "description": "Merge multiple files",
-            "default": "",
-            "properties": {
-                "filemerge_debug": {
-                    "type": "integer",
-                    "description": "Debug level for FileMerger step. Increase for verbose logging",
-                    "fa_icon": "fas fa-bug",
-                    "default": 0,
-                    "hidden": true
-                }
-            }
-        },
         "protein_inference": {
             "title": "Protein inference",
             "type": "object",
             "description": "To group proteins, calculate scores on the protein (group) level and to potentially modify associations from peptides to proteins.",
             "default": "",
             "properties": {
-                "protein_inference_bayesian": {
-                    "type": "boolean",
-                    "description": "Beyesian is used if protein inference is done with Epifany",
-                    "default": false,
+                "protein_inference_method": {
+                    "type": "string",
+                    "description": "The inference method to use. 'aggregation' (default) or 'bayesian'.",
+                    "default": "aggregation",
                     "fa_icon": "fas fa-list-ol",
-                    "hidden": true
+                    "help_text": "Infer proteins through:\n\n* 'aggregation'  =  aggregates all peptide scores across a protein (by calculating the maximum) (default)\n* 'bayesian'        =  compute a posterior probability for every protein based on a Bayesian network (i.e. using Epifany)\n* ('percolator' not yet supported)\n\n**Note:** If protein grouping is performed also depends on the `protein_quant` parameter (i.e. if peptides have to be unique or unique to a group only)",
+                    "enum": ["aggregation", "bayesian"]
+                },
+                "protein_level_fdr_cutoff": {
+                    "type": "number",
+                    "description": "The experiment-wide protein (group)-level FDR cutoff. Default: 0.05",
+                    "default": 0.01,
+                    "fa_icon": "fas fa-filter",
+                    "help_text": "This can be protein level if 'strictly_unique_peptides' are used for protein quantification. See [`--protein_quant`](#params_protein_quant)"
                 },
                 "picked_fdr": {
                     "type": "boolean",
                     "description": "Use picked protein FDRs",
                     "default": true,
-                    "fa_icon": "fas fa-list-ol",
-                    "hidden": true
+                    "fa_icon": "fas fa-list-ol"
                 },
                 "protein_score": {
                     "type": "string",
-                    "description": "How to aggregate scores of peptides matching to the same protein",
+                    "description": "[Ignored in Bayesian] How to aggregate scores of peptides matching to the same protein",
                     "default": "best",
-                    "enum": ["best", "product", "sum", "maximum"],
+                    "enum": ["best", "product", "sum"],
                     "fa_icon": "fas fa-list-ol"
                 },
+                "use_shared_peptides": {
+                    "type": "boolean",
+                    "description": "[Ignored in Bayesian] Also use shared peptides during score aggregation to protein level",
+                    "default": true,
+                    "fa_icon": "fas fa-filter"
+                },
                 "min_peptides_per_protein": {
                     "type": "integer",
                     "description": "[Ignored in Bayesian] Minimum number of peptides needed for a protein identification",
@@ -683,46 +579,20 @@
                 },
                 "top_PSMs": {
                     "type": "integer",
-                    "description": "Consider only top X PSMs per spectrum. 0 considers all.(Default 1).",
+                    "description": "Consider only the top X PSMs per spectrum to find the best PSM per peptide. 0 considers all.",
                     "default": 1,
                     "fa_icon": "fas fa-filter"
                 },
-                "greedy_group_resolution": {
-                    "type": "string",
-                    "description": "Post-process inference output with greedy resolution of shared peptides based on the parent protein probabilities. Also adds the resolved ambiguity groups to output.",
-                    "default": "none",
-                    "enum": ["none", "remove_associations_only", "remove_proteins_wo_evidence"]
-                },
-                "keep_best_PSM_only": {
-                    "type": "boolean",
-                    "description": "Epifany uses the best PSM per peptide for inference. Discard the rest (true) or keepe.g. for quantification/reporting?",
-                    "default": true,
-                    "fa_icon": "fas fa-list-ol"
-                },
                 "update_PSM_probabilities": {
                     "type": "boolean",
-                    "description": "(Experimental:) Update PSM probabilities with their posteriors under consideration of the protein probabilities.",
-                    "default": true,
-                    "fa_icon": "fas fa-list-ol"
-                },
-                "protein_level_fdr_cutoff": {
-                    "type": "number",
-                    "description": "The experiment-wide protein (group)-level FDR cutoff. Default: 0.05",
-                    "default": 0.01,
-                    "fa_icon": "fas fa-filter",
-                    "help_text": "This can be protein level if 'strictly_unique_peptides' are used for protein quantification. See [`--protein_quant`](#params_protein_quant)"
-                },
-                "protein_inference_method": {
-                    "type": "string",
-                    "description": "The inference method to use. 'aggregation' (default) or 'bayesian'.",
-                    "default": "aggregation",
+                    "description": "[Bayesian-only; Experimental] Update PSM probabilities with their posteriors under consideration of the protein probabilities.",
+                    "default": false,
                     "fa_icon": "fas fa-list-ol",
-                    "help_text": "Infer proteins through:\n\n* 'aggregation'  =  aggregates all peptide scores across a protein (by calculating the maximum) (default)\n* 'bayesian'        =  compute a posterior probability for every protein based on a Bayesian network (i.e. using Epifany)\n* ('percolator' not yet supported)\n\n**Note:** If protein grouping is performed also depends on the `protein_quant` parameter (i.e. if peptides have to be unique or unique to a group only)",
-                    "enum": ["aggregation", "bayesian"]
+                    "hidden": true
                 },
                 "protein_inference_debug": {
                     "type": "integer",
-                    "description": "Debug level for ProteinInferencer step. Increase for verbose logging",
+                    "description": "Debug level for the protein inference step. Increase for verbose logging",
                     "fa_icon": "fas fa-bug",
                     "default": 0,
                     "hidden": true
@@ -730,19 +600,12 @@
             },
             "fa_icon": "fab fa-hubspot"
         },
-        "protein_quantification": {
-            "title": "Protein Quantification",
+        "protein_quantification_dda": {
+            "title": "Protein Quantification (DDA)",
             "type": "object",
-            "description": "",
+            "description": "General protein quantification settings for both LFQ and Isobaric labelling.",
             "default": "",
             "properties": {
-                "conflict_resolver_debug": {
-                    "type": "integer",
-                    "description": "Debug level for IDConflictResolver step. Increase for verbose logging",
-                    "fa_icon": "fas fa-bug",
-                    "default": 0,
-                    "hidden": true
-                },
                 "top": {
                     "type": "integer",
                     "description": "Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all, Default 3)",
@@ -787,11 +650,20 @@
                 },
                 "protein_quant": {
                     "type": "string",
-                    "description": "Quantify proteins based on:\n\n* 'unique_peptides' = use peptides mapping to single proteins or a group of indistinguishable proteins (according to the set of experimentally identified peptides)\n* 'strictly_unique_peptides' = use peptides mapping to a unique single protein only\n* 'shared_peptides' = use shared peptides, too, but only greedily for its best group (by inference score)",
+                    "description": "Quantify proteins based on:\n\n* 'unique_peptides' = use peptides mapping to single proteins or a group of indistinguishable proteins (according to the set of experimentally identified peptides)\n* 'strictly_unique_peptides' (only LFQ) = use peptides mapping to a unique single protein only\n* 'shared_peptides' = use shared peptides, too, but only greedily for its best group (by inference score and nr. of peptides)",
                     "default": "unique_peptides",
                     "enum": ["unique_peptides", "strictly_unique_peptides", "shared_peptides"],
                     "fa_icon": "fas fa-list-ol"
-                },
+                }
+            },
+            "fa_icon": "fas fa-braille"
+        },
+        "protein_quantification_lfq": {
+            "title": "Protein Quantification (LFQ)",
+            "type": "object",
+            "description": "",
+            "default": "",
+            "properties": {
                 "quantification_method": {
                     "type": "string",
                     "description": "Choose between feature-based quantification based on integrated MS1 signals ('feature_intensity'; default) or spectral counting of PSMs ('spectral_counting'). **WARNING:** 'spectral_counting' is not compatible with our MSstats step yet. MSstats will therefore be disabled automatically with that choice.",
@@ -830,29 +702,102 @@
                     "default": false,
                     "fa_icon": "far fa-check-square"
                 },
-                "inf_quant_debug": {
+                "plfq_debug": {
                     "type": "integer",
                     "description": "Debug level when running the re-scoring. Logs become more verbose and at '>666' potentially very large temporary files are kept.",
                     "fa_icon": "fas fa-bug",
                     "hidden": true,
                     "default": 0
+                }
+            },
+            "fa_icon": "fas fa-braille"
+        },
+        "isobaric_analyzer": {
+            "title": "Isobaric analyzer",
+            "type": "object",
+            "description": "Extracts and normalizes labeling information",
+            "default": "",
+            "properties": {
+                "labelling_type": {
+                    "type": "string",
+                    "description": "Isobaric labelling method. Will be ignored if SDRF was given.",
+                    "fa_icon": "fas fa-font",
+                    "help_text": "Isobaric Quantification method used in the experiment.",
+                    "enum": [
+                        "label free sample",
+                        "itraq4plex",
+                        "itraq8plex",
+                        "tmt6plex",
+                        "tmt10plex",
+                        "tmt11plex",
+                        "tmt16plex"
+                    ]
+                },
+                "select_activation": {
+                    "type": "string",
+                    "description": "Operate only on MSn scans where any of its precursors features a certain activation method. Set to empty to disable.",
+                    "fa_icon": "fas fa-font",
+                    "enum": ["HCD", "CID", "ETD", "ECD"]
+                },
+                "reporter_mass_shift": {
+                    "type": "number",
+                    "description": "Allowed shift (left to right) in Th from the expected position",
+                    "default": 0.002,
+                    "fa_icon": "fas fa-sliders-h"
+                },
+                "min_precursor_intensity": {
+                    "type": "number",
+                    "description": "Minimum intensity of the precursor to be extracted",
+                    "default": 1.0,
+                    "fa_icon": "fas fa-sliders-h"
+                },
+                "min_precursor_purity": {
+                    "type": "number",
+                    "description": "Minimum fraction of the total intensity. 0.0:1.0",
+                    "default": 0.0,
+                    "fa_icon": "fas fa-sliders-h",
+                    "help_text": "Minimum fraction of the total intensity in the isolation window of the precursor spectrum"
+                },
+                "min_reporter_intensity": {
+                    "type": "number",
+                    "description": "Minimum intensity of the individual reporter ions to be extracted.",
+                    "default": 0.0,
+                    "fa_icon": "fas fa-sliders-h"
+                },
+                "precursor_isotope_deviation": {
+                    "type": "number",
+                    "description": "Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak",
+                    "default": 10.0,
+                    "fa_icon": "fas fa-sliders-h"
                 },
-                "proteinquant_debug": {
+                "isotope_correction": {
+                    "type": "boolean",
+                    "description": "Enable isotope correction (highly recommended)",
+                    "default": true,
+                    "fa_icon": "fas fa-toggle-on"
+                },
+                "iso_normalization": {
+                    "type": "boolean",
+                    "description": "Enable normalization of the channel intensities",
+                    "default": false,
+                    "fa_icon": "fas fa-toggle-on",
+                    "help_text": "The normalization is done by using the Median of Ratios. Also the ratios the medians is provided as control measure."
+                },
+                "reference_channel": {
                     "type": "integer",
-                    "description": "Debug level when running ProteinQuantifier.",
-                    "fa_icon": "fas fa-bug",
-                    "default": 0,
-                    "hidden": true
+                    "description": "The reference channel, e.g. for calculating ratios.",
+                    "fa_icon": "fas fa-list-ol",
+                    "default": 126
                 },
-                "msstatsconverter_debug": {
+                "iso_debug": {
                     "type": "integer",
-                    "description": "Debug level when running the re-scoring. Logs become more verbose and at '>666' potentially very large temporary files are kept.",
+                    "description": "Set the debug level",
                     "fa_icon": "fas fa-bug",
                     "default": 0,
                     "hidden": true
                 }
             },
-            "fa_icon": "fas fa-braille"
+            "fa_icon": "far fa-chart-bar"
         },
         "DIA-NN": {
             "title": "DIA-NN",
@@ -860,9 +805,9 @@
             "description": "Settings for DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing.",
             "default": "",
             "properties": {
-                "acqusition_method": {
+                "acquisition_method": {
                     "type": "string",
-                    "description": "Proteomics data acquistion method",
+                    "description": "Proteomics data acquisition method",
                     "default": "dda",
                     "enum": ["dda", "dia"],
                     "fa_icon": "far fa-list-ol"
@@ -903,7 +848,7 @@
                 },
                 "diann_normalize": {
                     "type": "boolean",
-                    "description": "Enable cross-run normalisation between runs by diann.",
+                    "description": "Enable cross-run normalization between runs by diann.",
                     "default": true,
                     "fa_icon": "far fa-check-square"
                 }
@@ -1149,18 +1094,12 @@
         {
             "$ref": "#/definitions/input_output_options"
         },
-        {
-            "$ref": "#/definitions/main_parameters_sdrf"
-        },
         {
             "$ref": "#/definitions/protein_database"
         },
         {
             "$ref": "#/definitions/spectrum_preprocessing"
         },
-        {
-            "$ref": "#/definitions/isobaric_analyzer"
-        },
         {
             "$ref": "#/definitions/database_search"
         },
@@ -1186,13 +1125,16 @@
             "$ref": "#/definitions/feature_mapper"
         },
         {
-            "$ref": "#/definitions/file_merge"
+            "$ref": "#/definitions/protein_inference"
+        },
+        {
+            "$ref": "#/definitions/protein_quantification_dda"
         },
         {
-            "$ref": "#/definitions/protein_inference"
+            "$ref": "#/definitions/protein_quantification_lfq"
         },
         {
-            "$ref": "#/definitions/protein_quantification"
+            "$ref": "#/definitions/isobaric_analyzer"
         },
         {
             "$ref": "#/definitions/DIA-NN"
diff --git a/subworkflows/local/create_input_channel.nf b/subworkflows/local/create_input_channel.nf
index 603b6c5f..7fccb3c4 100644
--- a/subworkflows/local/create_input_channel.nf
+++ b/subworkflows/local/create_input_channel.nf
@@ -6,7 +6,7 @@ include { PREPROCESS_EXPDESIGN } from '../../modules/local/preprocess_expdesign'
 
 class Wrapper {
     def labelling_type = ""
-    def acqusition_method = ""
+    def acquisition_method = ""
 }
 
 workflow CREATE_INPUT_CHANNEL {
@@ -36,12 +36,12 @@ workflow CREATE_INPUT_CHANNEL {
     // TODO remove. We can't use the variable to direct channels anyway
     wrapper = new Wrapper()
     wrapper.labelling_type = ""
-    wrapper.acqusition_method = ""
+    wrapper.acquisition_method = ""
 
     ch_in_design.splitCsv(header: true, sep: '\t')
             .map { create_meta_channel(it, is_sdrf, enzymes, files, wrapper) }
             .branch {
-                ch_meta_config_dia: it[0].acqusition_method.contains("dia")
+                ch_meta_config_dia: it[0].acquisition_method.contains("dia")
                 ch_meta_config_iso: it[0].labelling_type.contains("tmt") || it[0].labelling_type.contains("itraq")
                 ch_meta_config_lfq: it[0].labelling_type.contains("label free")
             }
@@ -55,7 +55,6 @@ workflow CREATE_INPUT_CHANNEL {
     ch_meta_config_lfq                     // [meta, [spectra_files ]]
     ch_meta_config_dia                     // [meta, [spectra files ]]
     ch_expdesign
-    wrapper.labelling_type
 
     version         = ch_versions
 }
@@ -103,17 +102,17 @@ def create_meta_channel(LinkedHashMap row, is_sdrf, enzymes, files, wrapper) {
         meta.fragmentmasstolerance      = params.fragment_mass_tolerance
         meta.fragmentmasstoleranceunit  = params.fragment_mass_tolerance_unit
         meta.enzyme                     = params.enzyme
-        meta.acqusition_method          = params.acqusition_method
+        meta.acquisition_method          = params.acquisition_method
     } else {
         if (row["Proteomics Data Acquisition Method"].contains("Data-Dependent Acquisition")) {
-            meta.acqusition_method = "dda"
+            meta.acquisition_method = "dda"
         } else if (row["Proteomics Data Acquisition Method"].contains("Data-Independent Acquisition")){
-            meta.acqusition_method = "dia"
+            meta.acquisition_method = "dia"
         } else {
             log.error "Currently DIA and DDA are supported for the pipeline. Check and Fix your SDRF."
             exit 1
         }
-        wrapper.acqusition_method       = meta.acqusition_method
+        wrapper.acquisition_method       = meta.acquisition_method
         meta.labelling_type             = row.Label
         meta.dissociationmethod         = row.DissociationMethod
         meta.fixedmodifications         = row.FixedModifications
@@ -132,8 +131,8 @@ def create_meta_channel(LinkedHashMap row, is_sdrf, enzymes, files, wrapper) {
             exit 1
         }
     }
-    if (meta.acqusition_method == "dia") {
-        log.warn "Acqusition Method: '${meta.acqusition_method}'"
+    if (meta.acquisition_method == "dia") {
+        log.warn "Acquisition Method: '${meta.acquisition_method}'"
     } else {
         log.warn "Label: '${meta.labelling_type}'"
         if (wrapper.labelling_type.equals("")) {
@@ -151,7 +150,7 @@ def create_meta_channel(LinkedHashMap row, is_sdrf, enzymes, files, wrapper) {
         }
     }
 
-    if (wrapper.labelling_type.contains("label free") || meta.acqusition_method == "dia") {
+    if (wrapper.labelling_type.contains("label free") || meta.acquisition_method == "dia") {
         if (filestr in files) {
             log.error "Currently only one search engine setting/DIA-NN setting per file is supported for the whole experiment. ${filestr} has multiple entries in your SDRF. Maybe you have a (isobaric) labelled experiment? Otherwise, consider splitting your design into multiple experiments."
             exit 1
diff --git a/subworkflows/local/databasesearchengines.nf b/subworkflows/local/databasesearchengines.nf
index 0224b674..ea7f0bf5 100644
--- a/subworkflows/local/databasesearchengines.nf
+++ b/subworkflows/local/databasesearchengines.nf
@@ -4,7 +4,6 @@
 
 include { SEARCHENGINEMSGF } from '../../modules/local/openms/thirdparty/searchenginemsgf/main'
 include { SEARCHENGINECOMET} from '../../modules/local/openms/thirdparty/searchenginecomet/main'
-include { INDEXPEPTIDES } from '../../modules/local/openms/indexpeptides/main'
 
 workflow DATABASESEARCHENGINES {
     take:
@@ -26,11 +25,8 @@ workflow DATABASESEARCHENGINES {
         ch_id_comet = ch_id_comet.mix(SEARCHENGINECOMET.out.id_files_comet)
     }
 
-    INDEXPEPTIDES(ch_id_msgf.mix(ch_id_comet).combine(searchengine_in_db))
-    ch_versions = ch_versions.mix(INDEXPEPTIDES.out.version)
-
     emit:
-    ch_id_files_idx = INDEXPEPTIDES.out.id_files_idx
+    ch_id_files_idx = ch_id_msgf.mix(ch_id_comet)
 
     versions        = ch_versions
 }
diff --git a/subworkflows/local/proteininference.nf b/subworkflows/local/proteininference.nf
index 05540e8f..5ee3f5f1 100644
--- a/subworkflows/local/proteininference.nf
+++ b/subworkflows/local/proteininference.nf
@@ -4,7 +4,7 @@
 
 include { EPIFANY } from '../../modules/local/openms/epifany/main'
 include { PROTEININFERENCE as PROTEININFERENCER} from '../../modules/local/openms/proteininference/main'
-include { IDFILTER as EPIFILTER } from '../../modules/local/openms/idfilter/main'
+include { IDFILTER } from '../../modules/local/openms/idfilter/main'
 
 workflow PROTEININFERENCE {
     take:
@@ -13,19 +13,19 @@ workflow PROTEININFERENCE {
     main:
     ch_version = Channel.empty()
 
-    if (params.protein_inference_bayesian) {
+    if (params.protein_inference_method == "bayesian") {
         EPIFANY(consus_file)
         ch_version = ch_version.mix(EPIFANY.out.version)
-        ch_epifilter = EPIFANY.out.epi_inference
+        ch_inference = EPIFANY.out.epi_inference
     } else {
         PROTEININFERENCER(consus_file)
         ch_version = ch_version.mix(PROTEININFERENCER.out.version)
-        ch_epifilter = PROTEININFERENCER.out.protein_inference
+        ch_inference = PROTEININFERENCER.out.protein_inference
     }
 
-    EPIFILTER(ch_epifilter)
-    ch_version = ch_version.mix(EPIFILTER.out.version)
-    EPIFILTER.out.id_filtered
+    IDFILTER(ch_inference)
+    ch_version = ch_version.mix(IDFILTER.out.version)
+    IDFILTER.out.id_filtered
         .multiMap{ it ->
             meta: it[0]
             results: it[1]
diff --git a/workflows/quantms.nf b/workflows/quantms.nf
index 0064f9e5..2493ddbf 100644
--- a/workflows/quantms.nf
+++ b/workflows/quantms.nf
@@ -42,7 +42,7 @@ include { PMULTIQC as SUMMARYPIPELINE } from '../modules/local/pmultiqc/main'
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //
 include { INPUT_CHECK } from '../subworkflows/local/input_check'
-include { FILE_PREPARATION as FILE_PREPARATION_LFQ; FILE_PREPARATION as FILE_PREPARATION_TMT; FILE_PREPARATION as FILE_PREPARATION_DIA } from '../subworkflows/local/file_preparation'
+include { FILE_PREPARATION } from '../subworkflows/local/file_preparation'
 include { CREATE_INPUT_CHANNEL } from '../subworkflows/local/create_input_channel'
 
 /*
@@ -91,57 +91,43 @@ workflow QUANTMS {
     //
     // SUBWORKFLOW: File preparation
     //
-    FILE_PREPARATION_TMT (
-        CREATE_INPUT_CHANNEL.out.ch_meta_config_iso
-    )
-    FILE_PREPARATION_LFQ (
-        CREATE_INPUT_CHANNEL.out.ch_meta_config_lfq
-    )
-
-    FILE_PREPARATION_DIA (
-        CREATE_INPUT_CHANNEL.out.ch_meta_config_dia
+    FILE_PREPARATION (
+        CREATE_INPUT_CHANNEL.out.ch_meta_config_iso.mix(CREATE_INPUT_CHANNEL.out.ch_meta_config_lfq).mix(CREATE_INPUT_CHANNEL.out.ch_meta_config_dia)
     )
 
-    ch_versions = ch_versions.mix(FILE_PREPARATION_TMT.out.version.ifEmpty(null))
-    ch_versions = ch_versions.mix(FILE_PREPARATION_LFQ.out.version.ifEmpty(null))
-    ch_versions = ch_versions.mix(FILE_PREPARATION_DIA.out.version.ifEmpty(null))
+    ch_versions = ch_versions.mix(FILE_PREPARATION.out.version.ifEmpty(null))
 
-    FILE_PREPARATION_LFQ.out.results
+    FILE_PREPARATION.out.results
         .map { it -> it[1] }
-        .set { ch_pmultiqc_mzmls_lfq }
+        .set { ch_pmultiqc_mzmls }
 
-    FILE_PREPARATION_TMT.out.results
-        .map { it -> it[1] }
-        .set { ch_pmultiqc_mzmls_iso }
+    FILE_PREPARATION.out.results
+            .branch {
+                dia: it[0].acquisition_method.contains("dia")
+                iso: it[0].labelling_type.contains("tmt") || it[0].labelling_type.contains("itraq")
+                lfq: it[0].labelling_type.contains("label free")
+            }
+            .set{ch_fileprep_result}
 
-    FILE_PREPARATION_DIA.out.results
-        .map { it -> it[1] }
-        .set { ch_pmultiqc_mzmls_dia }
-
-    ch_pmultiqc_mzmls = ch_pmultiqc_mzmls_lfq.mix(ch_pmultiqc_mzmls_iso).mix(ch_pmultiqc_mzmls_dia)
 
     //
     // WORKFLOW: Run main nf-core/quantms analysis pipeline based on the quantification type
     //
-    // TODO if we ever allow mixed labelling types, we need to split the files according to meta.labelling_type which contains
-    // labelling_type per file
     ch_pipeline_results = Channel.empty()
     ch_ids_pmultiqc = Channel.empty()
 
-    TMT(FILE_PREPARATION_TMT.out.results, CREATE_INPUT_CHANNEL.out.ch_expdesign)
+    TMT(ch_fileprep_result.iso, CREATE_INPUT_CHANNEL.out.ch_expdesign)
     ch_ids_pmultiqc = ch_ids_pmultiqc.mix(TMT.out.ch_pmultiqc_ids)
     ch_pipeline_results = ch_pipeline_results.mix(TMT.out.final_result)
     ch_versions = ch_versions.mix(TMT.out.versions.ifEmpty(null))
 
-    LFQ(FILE_PREPARATION_LFQ.out.results, CREATE_INPUT_CHANNEL.out.ch_expdesign)
+    LFQ(ch_fileprep_result.lfq, CREATE_INPUT_CHANNEL.out.ch_expdesign)
     ch_ids_pmultiqc = ch_ids_pmultiqc.mix(LFQ.out.ch_pmultiqc_ids)
     ch_pipeline_results = ch_pipeline_results.mix(LFQ.out.final_result)
     ch_versions = ch_versions.mix(LFQ.out.versions.ifEmpty(null))
 
-    DIA(FILE_PREPARATION_DIA.out.results, 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)
+    DIA(ch_fileprep_result.dia, CREATE_INPUT_CHANNEL.out.ch_expdesign)
+    ch_pipeline_results = ch_pipeline_results.mix(DIA.out.diann_report)
     ch_versions = ch_versions.mix(DIA.out.versions.ifEmpty(null))
 
 
@@ -166,10 +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()