Merge pull request #409 from ypriverol/dev

quantms-utils 0.0.8 -> 0.0.9
bigbio · Aug 17, 2024 · 58006d1 · 58006d1
2 parents 8cf493b + 9ae37c3
commit 58006d1
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Showing 12 changed files with 33 additions and 33 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,7 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Dependencies`
 
-- quantms-utils==0.0.8
+- quantms-utils==0.0.9
 - diann==1.9.1
 
 ### `Parameters`

diff --git a/modules/local/add_sage_feat/main.nf b/modules/local/add_sage_feat/main.nf
@@ -2,10 +2,10 @@ process SAGEFEATURE {
     tag "$meta.mzml_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.8"
+    conda "bioconda::quantms-utils=0.0.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(id_file), path(extra_feat)

diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf
@@ -2,10 +2,10 @@ process DIANNCONVERT {
     tag "$meta.experiment_id"
     label 'process_medium'
 
-    conda "bioconda::quantms-utils=0.0.8"
+    conda "bioconda::quantms-utils=0.0.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"
 
     input:
     path(report)

diff --git a/modules/local/extract_psm/main.nf b/modules/local/extract_psm/main.nf
@@ -2,17 +2,17 @@ process PSMCONVERSION {
     tag "$meta.mzml_id"
     label 'process_medium'
 
-    conda "bioconda::quantms-utils=0.0.8"
+    conda "bioconda::quantms-utils=0.0.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"
 
 
     input:
     tuple val(meta), path(idxml_file), path(spectrum_df)
 
     output:
-    path "*_psm.csv", emit: psm_info
+    path "*_psm.parquet", emit: psm_info
     path "versions.yml", emit: version
     path "*.log", emit: log
 

diff --git a/modules/local/extract_psm/meta.yml b/modules/local/extract_psm/meta.yml
@@ -25,7 +25,7 @@ output:
   - psm_info:
       type: file
       description: PSM csv file
-      pattern: "*_psm.csv"
+      pattern: "*_psm.parquet"
   - version:
       type: file
       description: File containing software version

diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf
@@ -2,10 +2,10 @@ process GENERATE_DIANN_CFG {
     tag "$meta.experiment_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.8"
+    conda "bioconda::quantms-utils=0.0.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"
 
     input:
     val(meta)

diff --git a/modules/local/ms2rescore/main.nf b/modules/local/ms2rescore/main.nf
@@ -2,10 +2,10 @@ process MS2RESCORE {
     tag "$meta.mzml_id"
     label 'process_high'
 
-    conda "bioconda::quantms-utils=0.0.8"
+    conda "bioconda::quantms-utils=0.0.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"
 
     // userEmulation settings when docker is specified
     containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : ''

diff --git a/modules/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf
@@ -3,10 +3,10 @@ process MZMLSTATISTICS {
     label 'process_medium'
     label 'process_single'
 
-    conda "bioconda::quantms-utils=0.0.8"
+    conda "bioconda::quantms-utils=0.0.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(ms_file)

diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf
@@ -6,10 +6,10 @@ process PREPROCESS_EXPDESIGN {
     tag "$design.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.8"
+    conda "bioconda::quantms-utils=0.0.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"
 
     input:
     path design

diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
@@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK {
     tag "$input_file"
     label 'process_single'
 
-    conda "bioconda::quantms-utils=0.0.8"
+    conda "bioconda::quantms-utils=0.0.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"
 
     input:
     path input_file

diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf
@@ -2,10 +2,10 @@ process SDRFPARSING {
     tag "$sdrf.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.8"
+    conda "bioconda::quantms-utils=0.0.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"
 
     input:
     path sdrf

diff --git a/modules/local/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf
@@ -2,10 +2,10 @@ process SPECTRUM2FEATURES {
     tag "$meta.mzml_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.8"
+    conda "bioconda::quantms-utils=0.0.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(id_file), path(ms_file)