Merge pull request #451 from ypriverol/dev

quanmts-utils 0.0.15 -> 0.0.17: ms2rescore bug solved
bigbio · Dec 4, 2024 · e50daae · e50daae
2 parents 0734320 + 9f764ad
commit e50daae
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Showing 12 changed files with 39 additions and 34 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -56,6 +56,11 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
+      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:

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=0.0.15"
+    conda "bioconda::quantms-utils=0.0.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' :
+        'biocontainers/quantms-utils:0.0.17--pyh7e72e81_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=0.0.15"
+    conda "bioconda::quantms-utils=0.0.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' :
+        'biocontainers/quantms-utils:0.0.17--pyh7e72e81_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=0.0.15"
+    conda "bioconda::quantms-utils=0.0.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' :
+        'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }"
 
 
     input:

diff --git a/modules/local/extract_sample/main.nf b/modules/local/extract_sample/main.nf
@@ -2,10 +2,10 @@ process GETSAMPLE {
     tag "$design.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.15"
+    conda "bioconda::quantms-utils=0.0.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' :
+        'biocontainers/quantms-utils:0.0.17--pyh7e72e81_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=0.0.15"
+    conda "bioconda::quantms-utils=0.0.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' :
+        'biocontainers/quantms-utils:0.0.17--pyh7e72e81_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=0.0.15"
+    conda "bioconda::quantms-rescoring=0.0.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-rescoring:0.0.1--pyhdfd78af_0' :
+        'biocontainers/quantms-rescoring:0.0.1--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' : ''
@@ -43,7 +43,7 @@ process MS2RESCORE {
     }
 
     """
-    quantmsutilsc ms2rescore \\
+    rescoring ms2rescore \\
         --psm_file $idxml \\
         --spectrum_path . \\
         --ms2_tolerance $ms2_tolerence \\

diff --git a/modules/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf
@@ -3,10 +3,10 @@ process MZMLSTATISTICS {
     label 'process_very_low'
     label 'process_single'
 
-    conda "bioconda::quantms-utils=0.0.15"
+    conda "bioconda::quantms-utils=0.0.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' :
+        'biocontainers/quantms-utils:0.0.17--pyh7e72e81_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=0.0.15"
+    conda "bioconda::quantms-utils=0.0.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' :
+        'biocontainers/quantms-utils:0.0.17--pyh7e72e81_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=0.0.15"
+    conda "bioconda::quantms-utils=0.0.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' :
+        'biocontainers/quantms-utils:0.0.17--pyh7e72e81_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=0.0.15"
+    conda "bioconda::quantms-utils=0.0.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' :
+        'biocontainers/quantms-utils:0.0.17--pyh7e72e81_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=0.0.15"
+    conda "bioconda::quantms-utils=0.0.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.17--pyh7e72e81_0' :
+        'biocontainers/quantms-utils:0.0.17--pyh7e72e81_0' }"
 
     input:
     tuple val(meta), path(id_file), path(ms_file)