0.0.6 -> 0.0.7

bigbio · Aug 13, 2024 · be1fb69 · be1fb69
1 parent d2621b3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,19 +8,30 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#386](https://github.com/bigbio/quantms/pull/386) Make validation of ontology terms optional
+- [#398](https://github.com/bigbio/quantms/pull/398) Python scripts moved to quantms-utils package
+- [#389](https://github.com/bigbio/quantms/pull/389) Introduction to DIANN 1.9.1 to the pipeline, only available in Singularity.
+- [#397](https://github.com/bigbio/quantms/pull/397) More options included in SDRF validation.
 
 ### Fixed
 
 - [#400](https://github.com/bigbio/quantms/pull/400) The random file selection when using `random_preanalysis` with DIANN is now reproducible.
 
 ### `Changed`
 
+- [#391](https://github.com/bigbio/quantms/pull/391) Move mzML statistics to parquet files from csv
+- [#386](https://github.com/bigbio/quantms/pull/386) Make optional the validation of ontology terms in the input SDRF file.
+- [#374](https://github.com/bigbio/quantms/pull/374) Create the common msgf+ database in one step before the msgf+ runs on each ms run file.
+-
+
 ### `Fixed`
 
 - [#396](https://github.com/bigbio/quantms/pull/396) Added verification of tar archive unpacking to prevent silent failures.
 
 ### `Dependencies`
 
+- quantms-utils==0.0.7
+- diann==1.9.1
+
 ### `Parameters`
 
 - `validate_ontologies`: enable or disable validating ontologies in the input SDRF file.

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=0.0.6"
+    conda "bioconda::quantms-utils=0.0.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.6--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.6--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.7--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.7--pyhdfd78af_0' }"
 
     input:
     path(report)

diff --git a/modules/local/extract_psm/main.nf b/modules/local/extract_psm/main.nf
@@ -2,10 +2,10 @@ process PSMCONVERSION {
     tag "$meta.mzml_id"
     label 'process_medium'
 
-    conda "bioconda::quantms-utils=0.0.6"
+    conda "bioconda::quantms-utils=0.0.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.6--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.6--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.7--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.7--pyhdfd78af_0' }"
 
 
     input:

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=0.0.6"
+    conda "bioconda::quantms-utils=0.0.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.6--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.6--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.7--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.7--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=0.0.6"
+    conda "bioconda::quantms-utils=0.0.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.6--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.6--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.7--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.7--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=0.0.6"
+    conda "bioconda::quantms-utils=0.0.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.6--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.6--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.7--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.7--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=0.0.6"
+    conda "bioconda::quantms-utils=0.0.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.6--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.6--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.7--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.7--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=0.0.6"
+    conda "bioconda::quantms-utils=0.0.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.6--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.6--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.7--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.7--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=0.0.6"
+    conda "bioconda::quantms-utils=0.0.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.6--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.6--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.7--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.7--pyhdfd78af_0' }"
 
     input:
     path sdrf