Merge pull request #43 from ypriverol/dev

improvements conda
bigbio · Nov 29, 2021 · 8056cf5 · 8056cf5
2 parents c707d7a + ccd9297
commit 8056cf5
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Showing 23 changed files with 46 additions and 23 deletions.
diff --git a/modules/local/openms/consensusid/main.nf b/modules/local/openms/consensusid/main.nf
@@ -12,7 +12,8 @@ process CONSENSUSID {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/decoydatabase/main.nf b/modules/local/openms/decoydatabase/main.nf
@@ -10,7 +10,8 @@ process DECOYDATABASE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/epifany/main.nf b/modules/local/openms/epifany/main.nf
@@ -10,7 +10,8 @@ process EPIFANY {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/extractpsmfeature/main.nf b/modules/local/openms/extractpsmfeature/main.nf
@@ -11,7 +11,8 @@ process EXTRACTPSMFEATURE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/falsediscoveryrate/main.nf b/modules/local/openms/falsediscoveryrate/main.nf
@@ -11,7 +11,8 @@ process FALSEDISCOVERYRATE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/filemerge/main.nf b/modules/local/openms/filemerge/main.nf
@@ -11,7 +11,8 @@ process FILEMERGE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/idconflictresolver/main.nf b/modules/local/openms/idconflictresolver/main.nf
@@ -10,7 +10,8 @@ process IDCONFLICTRESOLVER {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/idfilter/main.nf b/modules/local/openms/idfilter/main.nf
@@ -11,7 +11,8 @@ process IDFILTER {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/idmapper/main.nf b/modules/local/openms/idmapper/main.nf
@@ -11,7 +11,8 @@ process IDMAPPER {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/idpep/main.nf b/modules/local/openms/idpep/main.nf
@@ -10,7 +10,8 @@ process IDPEP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/idscoreswitcher/main.nf b/modules/local/openms/idscoreswitcher/main.nf
@@ -12,7 +12,8 @@ process IDSCORESWITCHER {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/indexpeptides/main.nf b/modules/local/openms/indexpeptides/main.nf
@@ -10,7 +10,8 @@ process INDEXPEPTIDES {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/isobaricanalyzer/main.nf b/modules/local/openms/isobaricanalyzer/main.nf
@@ -12,7 +12,8 @@ process ISOBARICANALYZER {
         pattern: "*.log",
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/msstatsconverter/main.nf b/modules/local/openms/msstatsconverter/main.nf
@@ -10,7 +10,8 @@ process MSSTATSCONVERTER {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/mzmlindexing/main.nf b/modules/local/openms/mzmlindexing/main.nf
@@ -11,7 +11,8 @@ process MZMLINDEXING {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         // TODO Need to built single container
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"

diff --git a/modules/local/openms/openmspeakpicker/main.nf b/modules/local/openms/openmspeakpicker/main.nf
@@ -12,7 +12,8 @@ process OPENMSPEAKPICKER {
         pattern: "*.log",
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/proteininference/main.nf b/modules/local/openms/proteininference/main.nf
@@ -10,7 +10,8 @@ process PROTEININFERENCE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/proteinquantifier/main.nf b/modules/local/openms/proteinquantifier/main.nf
@@ -10,7 +10,8 @@ process PROTEINQUANTIFIER {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/proteomicslfq/main.nf b/modules/local/openms/proteomicslfq/main.nf
@@ -10,7 +10,8 @@ process PROTEOMICSLFQ {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
     } else {

diff --git a/modules/local/openms/thirdparty/luciphoradapter/main.nf b/modules/local/openms/thirdparty/luciphoradapter/main.nf
@@ -11,7 +11,8 @@ process LUCIPHORADAPTER {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.6.0--0"
     } else {

diff --git a/modules/local/openms/thirdparty/percolator/main.nf b/modules/local/openms/thirdparty/percolator/main.nf
@@ -10,7 +10,8 @@ process PERCOLATOR {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
+    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 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
+bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.6.0--0"
     } else {