Merge pull request #2 from nf-core/dev

u
bigbio · Mar 31, 2022 · 2e4caef · 2e4caef
2 parents de7ea50 + 1727e4e
commit 2e4caef
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Showing 29 changed files with 276 additions and 339 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -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_lfq.config b/conf/test_lfq.config
@@ -25,5 +25,5 @@ params {
     enable_qc = true
     add_triqler_output = true
     protein_level_fdr_cutoff = 1.0
-    acqusition_method = "dda"
+    acquisition_method = "dda"
 }
diff --git a/modules/local/openms/consensusid/main.nf b/modules/local/openms/consensusid/main.nf
@@ -5,8 +5,8 @@ process CONSENSUSID {
 
     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
@@ -2,8 +2,8 @@ process DECOYDATABASE {
     label 'process_very_low'
     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
@@ -2,10 +2,10 @@ process EPIFANY {
     label 'process_medium'
     publishDir "${params.outdir}",
 
-    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=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 +17,24 @@ 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
@@ -4,8 +4,8 @@ process EXTRACTPSMFEATURES {
 
     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
@@ -4,8 +4,8 @@ process FALSEDISCOVERYRATE {
 
     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
@@ -4,8 +4,8 @@ process FILEMERGE {
 
     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 +24,9 @@ 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
@@ -3,8 +3,8 @@ process IDCONFLICTRESOLVER {
 
     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 +21,8 @@ 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
@@ -4,8 +4,8 @@ process IDFILTER {
 
     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 +25,6 @@ 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
@@ -4,8 +4,8 @@ process IDMAPPER {
 
     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 +24,8 @@ 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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)