update: nextflow

bigbio · Nov 19, 2024 · f4d1bce · f4d1bce
1 parent b791359
commit f4d1bce
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Showing 5 changed files with 55 additions and 5 deletions.
diff --git a/nextflow/maxquant_psm.nf b/nextflow/maxquant_psm.nf
@@ -0,0 +1,50 @@
+nextflow.enable.dsl=2
+
+params.msms_file 
+params.mzml_dir 
+params.output_dir
+params.chunksize = 1000000
+params.output_prefix_file = "psm"
+params.file_num = 20
+params.partitions = ""
+
+workflow {
+    generateResults(params.msms_file, params.output_dir, params.chunksize, params.output_prefix_file)
+    extractInfoFromMzml(generateResults.out, params.mzml_dir, params.output_dir, params.file_num, params.partitions)
+
+}
+process generateResults {
+    input:
+    path msmsFile
+    path outputDir
+    val chunksize
+    val output_prefix_file
+
+    output:
+    path "**/*.psm.parquet", emit: 'psm'
+
+    script:
+    """
+    quantmsioc convert-maxquant-psm --msms_file ${msmsFile} --output_folder ${outputDir} --chunksize ${chunksize} --output_prefix_file ${output_prefix_file}
+    """
+}
+
+process extractInfoFromMzml {
+    input:
+    path resultsFile
+    path mzmlDir
+    path outputDir
+    val file_num
+    val partitions
+
+    script:
+    if (partitions != ''){
+        """
+        quantmsioc map-spectrum-message-to-parquet --parquet_path ${resultsFile} --mzml_directory ${mzmlDir} --output_folder res/${outputDir} --file_num ${file_num} --partitions ${partitions}
+        """
+    }else {
+        """
+        quantmsioc map-spectrum-message-to-parquet --parquet_path ${resultsFile} --mzml_directory ${mzmlDir} --output_folder res/${outputDir} --file_num ${file_num}
+        """
+    }
+}
diff --git a/quantmsio/commands/diann_command.py b/quantmsio/commands/diann_command.py
@@ -85,7 +85,7 @@ def diann_convert_to_parquet(
         os.makedirs(output_folder)
 
     if not output_prefix_file:
-        output_prefix_file = ""
+        output_prefix_file = "feature"
     filename = create_uuid_filename(output_prefix_file, ".feature.parquet")
     feature_output_path = output_folder + "/" + filename
 

diff --git a/quantmsio/commands/feature_command.py b/quantmsio/commands/feature_command.py
@@ -78,7 +78,7 @@ def convert_feature_file(
         raise click.UsageError("Please provide all the required parameters")
     feature_manager = Feature(mzTab_path=mztab_file, sdrf_path=sdrf_file, msstats_in_path=msstats_file)
     if not output_prefix_file:
-        output_prefix_file = ""
+        output_prefix_file = "feature"
     filename = create_uuid_filename(output_prefix_file, ".feature.parquet")
     output_path = output_folder + "/" + filename
     if not partitions:

diff --git a/quantmsio/commands/maxquant_command.py b/quantmsio/commands/maxquant_command.py
@@ -45,7 +45,7 @@ def convert_maxquant_psm(
         raise click.UsageError("Please provide all the required parameters")
 
     if not output_prefix_file:
-        output_prefix_file = ""
+        output_prefix_file = "psm"
 
     MQ = MaxQuant()
     output_path = output_folder + "/" + create_uuid_filename(output_prefix_file, ".psm.parquet")
@@ -114,7 +114,7 @@ def convert_maxquant_feature(
         raise click.UsageError("Please provide all the required parameters")
 
     if not output_prefix_file:
-        output_prefix_file = ""
+        output_prefix_file = "feature"
 
     MQ = MaxQuant()
     filename = create_uuid_filename(output_prefix_file, ".feature.parquet")

diff --git a/quantmsio/commands/psm_command.py b/quantmsio/commands/psm_command.py
@@ -52,7 +52,7 @@ def convert_psm_file(
         raise click.UsageError("Please provide all the required parameters")
 
     if not output_prefix_file:
-        output_prefix_file = ""
+        output_prefix_file = "psm"
 
     psm_manager = Psm(mzTab_path=mztab_file)
     output_path = output_folder + "/" + create_uuid_filename(output_prefix_file, ".psm.parquet")