Merge pull request #81 from ypriverol/dev

Dev
bigbio · Mar 20, 2023 · 20db317 · 20db317
2 parents fba10ef + e0a5aae
commit 20db317
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diff --git a/bin/msstats_plfq.R b/bin/msstats_plfq.R
@@ -1,5 +1,9 @@
 #!/usr/bin/env Rscript
 
+# R script to run MSstats for LFQ data.
+# License: Apache 2.0
+# Author: Dai Chengxin, Julianus Pfeuffer, Yasset Perez-Riverol
+
 # load the MSstats library
 require(MSstats)
 require(tibble)

diff --git a/bin/msstats_tmt.R b/bin/msstats_tmt.R
@@ -1,4 +1,9 @@
 #!/usr/bin/env Rscript
+
+# R script to run MSstatsTMT for TMT data.
+# License: Apache 2.0
+# Author: Dai Chengxin, Julianus Pfeuffer, Yasset Perez-Riverol
+
 require(MSstatsTMT)
 require(stats)
 require(gplots)

diff --git a/bin/mzml_statistics.py b/bin/mzml_statistics.py
@@ -1,5 +1,9 @@
 #!/usr/bin/env python
-
+"""
+This script parse and mzml and generates a set of statistics about the file.
+License: Apache 2.0
+Authors: Hong Wong, Yasset Perez-Riverol
+"""
 import sys
 from pathlib import Path
 

diff --git a/bin/prepare_diann_parameters.py b/bin/prepare_diann_parameters.py
@@ -1,5 +1,11 @@
 #!/usr/bin/env python
 
+"""
+This script converts SDRF parameters to DIA-NN parameters
+License: Apache 2.0
+Authors: Dai Chengxin, Yasset Perez-Riverol
+"""
+
 import re
 from typing import List, Tuple
 

diff --git a/modules/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf
@@ -1,7 +1,7 @@
 process MZMLSTATISTICS {
     tag "$meta.mzml_id"
     label 'process_medium'
-    label 'process_single_thread'
+    label 'process_single'
 
     conda "bioconda::pyopenms=2.8.0"
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

diff --git a/modules/local/openms/consensusid/main.nf b/modules/local/openms/consensusid/main.nf
@@ -1,8 +1,7 @@
 process CONSENSUSID {
     tag "$meta.mzml_id"
     label 'process_medium'
-    // TODO could be easily parallelized
-    label 'process_single_thread'
+    label 'process_single'
     label 'openms'
 
     conda "bioconda::openms=2.9.1"

diff --git a/modules/local/openms/extractpsmfeatures/main.nf b/modules/local/openms/extractpsmfeatures/main.nf
@@ -1,7 +1,7 @@
 process EXTRACTPSMFEATURES {
     tag "$meta.mzml_id"
     label 'process_very_low'
-    label 'process_single_thread'
+    label 'process_single'
     label 'openms'
 
     conda "bioconda::openms=2.9.1"

diff --git a/modules/local/openms/falsediscoveryrate/main.nf b/modules/local/openms/falsediscoveryrate/main.nf
@@ -1,7 +1,7 @@
 process FALSEDISCOVERYRATE {
     tag "$meta.mzml_id"
     label 'process_low'
-    label 'process_single_thread'
+    label 'process_single'
     label 'openms'
 
     conda "bioconda::openms=2.9.1"

diff --git a/modules/local/openms/filemerge/main.nf b/modules/local/openms/filemerge/main.nf
@@ -1,6 +1,6 @@
 process FILEMERGE {
     label 'process_medium'
-    label 'process_single_thread'
+    label 'process_single'
     label 'openms'
 
     conda "bioconda::openms=2.9.1"

diff --git a/modules/local/openms/idfilter/main.nf b/modules/local/openms/idfilter/main.nf
@@ -1,7 +1,7 @@
 process IDFILTER {
     tag {task.ext.suffix == ".idXML" ? "$meta.mzml_id" : "$id_file.baseName"}
     label 'process_very_low'
-    label 'process_single_thread'
+    label 'process_single'
     label 'openms'
 
     conda "bioconda::openms=2.9.1"

diff --git a/modules/local/openms/idscoreswitcher/main.nf b/modules/local/openms/idscoreswitcher/main.nf
@@ -1,7 +1,7 @@
 process IDSCORESWITCHER {
     tag "$meta.mzml_id"
     label 'process_very_low'
-    label 'process_single_thread'
+    label 'process_single'
 
     conda "bioconda::openms=2.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

diff --git a/modules/local/thermorawfileparser/main.nf b/modules/local/thermorawfileparser/main.nf
@@ -1,7 +1,7 @@
 process THERMORAWFILEPARSER {
     tag "$meta.mzml_id"
     label 'process_low'
-    label 'process_single_thread'
+    label 'process_single'
     label 'error_retry'
 
     conda "conda-forge::mono bioconda::thermorawfileparser=1.3.4"