From ee02feb5fd61dfc0c9c6d5525b5beb432e216f50 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Wed, 24 Dec 2025 20:53:58 +0800
Subject: [PATCH 01/11] move thermorawfileparser from local to bigbio nf-core

---
 .../thermorawfileparser/environment.yml       |  7 ++
 modules/bigbio/thermorawfileparser/main.nf    | 67 +++++++++++++++++++
 modules/bigbio/thermorawfileparser/meta.nf    | 49 ++++++++++++++
 .../thermorawfileparser/tests/main.nf.test    | 53 +++++++++++++++
 .../tests/main.nf.test.snap                   | 26 +++++++
 .../thermorawfileparser/tests/nextflow.config |  3 +
 6 files changed, 205 insertions(+)
 create mode 100644 modules/bigbio/thermorawfileparser/environment.yml
 create mode 100644 modules/bigbio/thermorawfileparser/main.nf
 create mode 100644 modules/bigbio/thermorawfileparser/meta.nf
 create mode 100644 modules/bigbio/thermorawfileparser/tests/main.nf.test
 create mode 100644 modules/bigbio/thermorawfileparser/tests/main.nf.test.snap
 create mode 100644 modules/bigbio/thermorawfileparser/tests/nextflow.config

diff --git a/modules/bigbio/thermorawfileparser/environment.yml b/modules/bigbio/thermorawfileparser/environment.yml
new file mode 100644
index 00000000..ef0ac1ea
--- /dev/null
+++ b/modules/bigbio/thermorawfileparser/environment.yml
@@ -0,0 +1,7 @@
+name: thermorawfileparser
+channels:
+    - conda-forge
+    - bioconda
+    - defaults
+dependencies:
+    - bioconda::thermorawfileparser=1.4.5
\ No newline at end of file
diff --git a/modules/bigbio/thermorawfileparser/main.nf b/modules/bigbio/thermorawfileparser/main.nf
new file mode 100644
index 00000000..b395ae4b
--- /dev/null
+++ b/modules/bigbio/thermorawfileparser/main.nf
@@ -0,0 +1,67 @@
+process THERMORAWFILEPARSER {
+    tag "$meta.mzml_id"
+    label 'process_low'
+    label 'process_single'
+    label 'error_retry'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/thermorawfileparser:1.4.5--h05cac1d_1' :
+        'biocontainers/thermorawfileparser:1.4.5--h05cac1d_1' }"
+
+    stageInMode {
+        if (task.attempt == 1) {
+            if (task.executor == "awsbatch") {
+                'symlink'
+            } else {
+                'link'
+            }
+        } else if (task.attempt == 2) {
+            if (task.executor == "awsbatch") {
+                'copy'
+            } else {
+                'symlink'
+            }
+        } else {
+            'copy'
+        }
+    }
+    input:
+    tuple val(meta), path(rawfile)
+
+    output:
+    tuple val(meta), path("*.{mzML,mgf,parquet}"), emit: convert_files
+    path "versions.yml",   emit: versions
+    path "*.log",   emit: log
+
+    script:
+    def args = task.ext.args ?: ''
+    // Default to indexed mzML format (-f=2) if not specified in args
+    def formatArg = args.contains('-f=') ? '' : '-f=2'
+
+    """
+    ThermoRawFileParser.sh -i='${rawfile}' ${formatArg} ${args} -o=./ 2>&1 | tee '${rawfile.baseName}_conversion.log'
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ThermoRawFileParser: \$(ThermoRawFileParser.sh --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.mzml_id}"
+    def args = task.ext.args ?: ''
+    // Determine output format from args, default to mzML
+    // Format 0 = MGF, formats 1-2 = mzML, format 3 = Parquet, format 4 = None
+    def outputExt = (args =~ /-f=0\b/).find() ? 'mgf' : 'mzML'
+
+    """
+    touch '${prefix}.${outputExt}'
+    touch '${prefix}_conversion.log'
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ThermoRawFileParser: \$(ThermoRawFileParser.sh --version)
+    END_VERSIONS
+    """
+}
\ No newline at end of file
diff --git a/modules/bigbio/thermorawfileparser/meta.nf b/modules/bigbio/thermorawfileparser/meta.nf
new file mode 100644
index 00000000..53692b98
--- /dev/null
+++ b/modules/bigbio/thermorawfileparser/meta.nf
@@ -0,0 +1,49 @@
+name: thermorawfileparser
+description: Convert RAW file to mzML or MGF files
+keywords:
+    - raw
+    - mzML
+    - MGF
+    - OpenMS
+tools:
+    - thermorawfileparser:
+          description: |
+              ThermoRawFileParser converts Thermo RAW files to open standard formats like mzML, producing indexed output files.
+              Use `task.ext.args` to pass additional arguments, e.g.:
+              - `-f=0` for MGF output, `-f=1` for mzML, `-f=2` for indexed mzML (default), `-f=3` for Parquet, `-f=4` for None
+              - `-L` or `--msLevel=VALUE` to select MS levels (e.g., `-L=1,2` or `--msLevel=1-3`)
+          homepage: https://github.com/compomics/ThermoRawFileParser
+          documentation: https://github.com/compomics/ThermoRawFileParser
+input:
+    - meta:
+          type: map
+          description: |
+              Groovy Map containing sample information
+    - rawfile:
+          type: file
+          description: |
+              Thermo RAW file
+          pattern: "*.{raw,RAW}"
+output:
+    - meta:
+          type: map
+          description: |
+              Groovy Map containing sample information
+              e.g. [ id:'sample1', mzml_id:'UPS1_50amol_R3' ]
+    - convert_files:
+          type: file
+          description: |
+              Converted files in mzML or MGF format depending on the format parameter (-f).
+              Format options: 0 for MGF, 1 for mzML, 2 for indexed mzML (default), 3 for Parquet, 4 for None.
+          pattern: "*.{mzML,mgf}"
+    - log:
+          type: file
+          description: log file
+          pattern: "*.log"
+    - versions:
+          type: file
+          description: File containing software version
+          pattern: "versions.yml"
+authors:
+    - "@daichengxin"
+    - "@ypriverol"
\ No newline at end of file
diff --git a/modules/bigbio/thermorawfileparser/tests/main.nf.test b/modules/bigbio/thermorawfileparser/tests/main.nf.test
new file mode 100644
index 00000000..63e38ab9
--- /dev/null
+++ b/modules/bigbio/thermorawfileparser/tests/main.nf.test
@@ -0,0 +1,53 @@
+nextflow_process {
+
+    name "Test Process THERMORAWFILEPARSER"
+    script "../main.nf"
+    process "THERMORAWFILEPARSER"
+    tag "modules"
+    tag "modules_bigbio"
+    tag "thermorawfileparser"
+
+    test("Should convert RAW to mzML") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', mzml_id: 'UPS1_50amol_R3' ],
+                    file(params.test_data['proteomics']['msspectra']['ups1_50amol_r3'], checkIfExists: false)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out.versions).match("versions")
+            assert new File(process.out.convert_files[0][1]).name == 'TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML'
+            assert process.out.log.size() == 1
+        }
+    }
+
+    test("Should run stub mode") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', mzml_id: 'test_sample' ],
+                    file(params.test_data['proteomics']['msspectra']['ups1_50amol_r3'], checkIfExists: false)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out.versions).match("versions_stub")
+            assert new File(process.out.convert_files[0][1]).name == 'test_sample.mzML'
+            assert process.out.log.size() == 1
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/bigbio/thermorawfileparser/tests/main.nf.test.snap b/modules/bigbio/thermorawfileparser/tests/main.nf.test.snap
new file mode 100644
index 00000000..4b72682c
--- /dev/null
+++ b/modules/bigbio/thermorawfileparser/tests/main.nf.test.snap
@@ -0,0 +1,26 @@
+{
+  "versions": {
+    "content": [
+      [
+        "versions.yml:md5,dc9625538c025d615109ef8cac3a86ab"
+      ]
+    ],
+    "meta": {
+      "nf-test": "0.9.3",
+      "nextflow": "25.04.8"
+    },
+    "timestamp": "2025-12-11T06:27:00.000000"
+  },
+  "versions_stub": {
+    "content": [
+      [
+        "versions.yml:md5,dc9625538c025d615109ef8cac3a86ab"
+      ]
+    ],
+    "meta": {
+      "nf-test": "0.9.3",
+      "nextflow": "25.04.8"
+    },
+    "timestamp": "2025-12-11T06:27:00.000000"
+  }
+}
\ No newline at end of file
diff --git a/modules/bigbio/thermorawfileparser/tests/nextflow.config b/modules/bigbio/thermorawfileparser/tests/nextflow.config
new file mode 100644
index 00000000..3d148873
--- /dev/null
+++ b/modules/bigbio/thermorawfileparser/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+}
\ No newline at end of file

From 2c1e8dad153ac97743c2cbb25832eb270619c528 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Thu, 25 Dec 2025 11:09:31 +0800
Subject: [PATCH 02/11] Update modules.json

---
 modules.json | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/modules.json b/modules.json
index 03b49c8c..1aaf5630 100644
--- a/modules.json
+++ b/modules.json
@@ -36,6 +36,17 @@
                     }
                 }
             }
+        },
+        "https://github.com/bigbio/nf-modules.git": {
+            "modules": {
+                "bigbio": {
+                    "thermorawfileparser": {
+                        "branch": "main",
+                        "git_sha": "db15a4b1231caee00e74a6d50b7d3f98e076e24d",
+                        "installed_by": ["modules"]
+                    }
+                }
+            }
         }
     }
 }

From f02bc8a05d7abf396918d39beb8b64664090400c Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Thu, 25 Dec 2025 12:44:52 +0800
Subject: [PATCH 03/11] Update environment.yml

---
 modules/bigbio/thermorawfileparser/environment.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/bigbio/thermorawfileparser/environment.yml b/modules/bigbio/thermorawfileparser/environment.yml
index ef0ac1ea..63b8fc64 100644
--- a/modules/bigbio/thermorawfileparser/environment.yml
+++ b/modules/bigbio/thermorawfileparser/environment.yml
@@ -1,7 +1,7 @@
 name: thermorawfileparser
 channels:
-    - conda-forge
-    - bioconda
-    - defaults
+  - conda-forge
+  - bioconda
+  - defaults
 dependencies:
-    - bioconda::thermorawfileparser=1.4.5
\ No newline at end of file
+  - bioconda::thermorawfileparser=1.4.5

From 32cdbc4245795da0983895c7d1b0d8a9aabdab5c Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Thu, 25 Dec 2025 13:24:10 +0800
Subject: [PATCH 04/11] fixed

---
 modules/bigbio/thermorawfileparser/main.nf               | 2 +-
 modules/bigbio/thermorawfileparser/meta.nf               | 2 +-
 modules/bigbio/thermorawfileparser/tests/main.nf.test    | 2 +-
 modules/bigbio/thermorawfileparser/tests/nextflow.config | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/bigbio/thermorawfileparser/main.nf b/modules/bigbio/thermorawfileparser/main.nf
index b395ae4b..31ce4d0b 100644
--- a/modules/bigbio/thermorawfileparser/main.nf
+++ b/modules/bigbio/thermorawfileparser/main.nf
@@ -64,4 +64,4 @@ process THERMORAWFILEPARSER {
         ThermoRawFileParser: \$(ThermoRawFileParser.sh --version)
     END_VERSIONS
     """
-}
\ No newline at end of file
+}
diff --git a/modules/bigbio/thermorawfileparser/meta.nf b/modules/bigbio/thermorawfileparser/meta.nf
index 53692b98..50289e92 100644
--- a/modules/bigbio/thermorawfileparser/meta.nf
+++ b/modules/bigbio/thermorawfileparser/meta.nf
@@ -46,4 +46,4 @@ output:
           pattern: "versions.yml"
 authors:
     - "@daichengxin"
-    - "@ypriverol"
\ No newline at end of file
+    - "@ypriverol"
diff --git a/modules/bigbio/thermorawfileparser/tests/main.nf.test b/modules/bigbio/thermorawfileparser/tests/main.nf.test
index 63e38ab9..355fbb15 100644
--- a/modules/bigbio/thermorawfileparser/tests/main.nf.test
+++ b/modules/bigbio/thermorawfileparser/tests/main.nf.test
@@ -50,4 +50,4 @@ nextflow_process {
             assert process.out.log.size() == 1
         }
     }
-}
\ No newline at end of file
+}
diff --git a/modules/bigbio/thermorawfileparser/tests/nextflow.config b/modules/bigbio/thermorawfileparser/tests/nextflow.config
index 3d148873..0293c16f 100644
--- a/modules/bigbio/thermorawfileparser/tests/nextflow.config
+++ b/modules/bigbio/thermorawfileparser/tests/nextflow.config
@@ -1,3 +1,3 @@
 process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-}
\ No newline at end of file
+}

From eb53e439373d6a07f17d07c098f3ef3574ad7030 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 27 Dec 2025 17:54:06 +0800
Subject: [PATCH 05/11] Update modules.json

---
 modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index 1aaf5630..a4517edf 100644
--- a/modules.json
+++ b/modules.json
@@ -42,7 +42,7 @@
                 "bigbio": {
                     "thermorawfileparser": {
                         "branch": "main",
-                        "git_sha": "db15a4b1231caee00e74a6d50b7d3f98e076e24d",
+                        "git_sha": "af29ddced3096d84d6158afc342bdc2fc009f2f1",
                         "installed_by": ["modules"]
                     }
                 }

From 13556f8e17e85742494b7ac8d92aa5b912b15ca8 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 27 Dec 2025 18:19:54 +0800
Subject: [PATCH 06/11] fixed

---
 modules/bigbio/thermorawfileparser/{meta.nf => meta.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename modules/bigbio/thermorawfileparser/{meta.nf => meta.yml} (100%)

diff --git a/modules/bigbio/thermorawfileparser/meta.nf b/modules/bigbio/thermorawfileparser/meta.yml
similarity index 100%
rename from modules/bigbio/thermorawfileparser/meta.nf
rename to modules/bigbio/thermorawfileparser/meta.yml

From 2a43944b9c4268da6726a7eba063400e89b507fb Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 27 Dec 2025 18:24:47 +0800
Subject: [PATCH 07/11] Update meta.yml

---
 modules/bigbio/thermorawfileparser/meta.yml | 84 ++++++++++-----------
 1 file changed, 42 insertions(+), 42 deletions(-)

diff --git a/modules/bigbio/thermorawfileparser/meta.yml b/modules/bigbio/thermorawfileparser/meta.yml
index 50289e92..0ab076f9 100644
--- a/modules/bigbio/thermorawfileparser/meta.yml
+++ b/modules/bigbio/thermorawfileparser/meta.yml
@@ -1,49 +1,49 @@
 name: thermorawfileparser
 description: Convert RAW file to mzML or MGF files
 keywords:
-    - raw
-    - mzML
-    - MGF
-    - OpenMS
+  - raw
+  - mzML
+  - MGF
+  - OpenMS
 tools:
-    - thermorawfileparser:
-          description: |
-              ThermoRawFileParser converts Thermo RAW files to open standard formats like mzML, producing indexed output files.
-              Use `task.ext.args` to pass additional arguments, e.g.:
-              - `-f=0` for MGF output, `-f=1` for mzML, `-f=2` for indexed mzML (default), `-f=3` for Parquet, `-f=4` for None
-              - `-L` or `--msLevel=VALUE` to select MS levels (e.g., `-L=1,2` or `--msLevel=1-3`)
-          homepage: https://github.com/compomics/ThermoRawFileParser
-          documentation: https://github.com/compomics/ThermoRawFileParser
+  - thermorawfileparser:
+      description: |
+        ThermoRawFileParser converts Thermo RAW files to open standard formats like mzML, producing indexed output files.
+        Use `task.ext.args` to pass additional arguments, e.g.:
+        - `-f=0` for MGF output, `-f=1` for mzML, `-f=2` for indexed mzML (default), `-f=3` for Parquet, `-f=4` for None
+        - `-L` or `--msLevel=VALUE` to select MS levels (e.g., `-L=1,2` or `--msLevel=1-3`)
+      homepage: https://github.com/compomics/ThermoRawFileParser
+      documentation: https://github.com/compomics/ThermoRawFileParser
 input:
-    - meta:
-          type: map
-          description: |
-              Groovy Map containing sample information
-    - rawfile:
-          type: file
-          description: |
-              Thermo RAW file
-          pattern: "*.{raw,RAW}"
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+  - rawfile:
+      type: file
+      description: |
+        Thermo RAW file
+      pattern: "*.{raw,RAW}"
 output:
-    - meta:
-          type: map
-          description: |
-              Groovy Map containing sample information
-              e.g. [ id:'sample1', mzml_id:'UPS1_50amol_R3' ]
-    - convert_files:
-          type: file
-          description: |
-              Converted files in mzML or MGF format depending on the format parameter (-f).
-              Format options: 0 for MGF, 1 for mzML, 2 for indexed mzML (default), 3 for Parquet, 4 for None.
-          pattern: "*.{mzML,mgf}"
-    - log:
-          type: file
-          description: log file
-          pattern: "*.log"
-    - versions:
-          type: file
-          description: File containing software version
-          pattern: "versions.yml"
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'sample1', mzml_id:'UPS1_50amol_R3' ]
+  - convert_files:
+      type: file
+      description: |
+        Converted files in mzML or MGF format depending on the format parameter (-f).
+        Format options: 0 for MGF, 1 for mzML, 2 for indexed mzML (default), 3 for Parquet, 4 for None.
+      pattern: "*.{mzML,mgf}"
+  - log:
+      type: file
+      description: log file
+      pattern: "*.log"
+  - versions:
+      type: file
+      description: File containing software version
+      pattern: "versions.yml"
 authors:
-    - "@daichengxin"
-    - "@ypriverol"
+  - "@daichengxin"
+  - "@ypriverol"

From 68b2090b456143ab3c720da6d99f9c61227eb6f7 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 27 Dec 2025 19:06:10 +0800
Subject: [PATCH 08/11] sysc

---
 modules.json                                               | 2 +-
 modules/bigbio/thermorawfileparser/main.nf                 | 1 +
 modules/bigbio/thermorawfileparser/tests/main.nf.test      | 1 +
 modules/bigbio/thermorawfileparser/tests/main.nf.test.snap | 2 +-
 modules/bigbio/thermorawfileparser/tests/nextflow.config   | 1 +
 5 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/modules.json b/modules.json
index a4517edf..5c371b97 100644
--- a/modules.json
+++ b/modules.json
@@ -42,7 +42,7 @@
                 "bigbio": {
                     "thermorawfileparser": {
                         "branch": "main",
-                        "git_sha": "af29ddced3096d84d6158afc342bdc2fc009f2f1",
+                        "git_sha": "57e0bbeaef79f0aaecad6848e334859f39ac268a",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/bigbio/thermorawfileparser/main.nf b/modules/bigbio/thermorawfileparser/main.nf
index 31ce4d0b..5004530a 100644
--- a/modules/bigbio/thermorawfileparser/main.nf
+++ b/modules/bigbio/thermorawfileparser/main.nf
@@ -65,3 +65,4 @@ process THERMORAWFILEPARSER {
     END_VERSIONS
     """
 }
+
diff --git a/modules/bigbio/thermorawfileparser/tests/main.nf.test b/modules/bigbio/thermorawfileparser/tests/main.nf.test
index 355fbb15..1646f737 100644
--- a/modules/bigbio/thermorawfileparser/tests/main.nf.test
+++ b/modules/bigbio/thermorawfileparser/tests/main.nf.test
@@ -51,3 +51,4 @@ nextflow_process {
         }
     }
 }
+
diff --git a/modules/bigbio/thermorawfileparser/tests/main.nf.test.snap b/modules/bigbio/thermorawfileparser/tests/main.nf.test.snap
index 4b72682c..6562491e 100644
--- a/modules/bigbio/thermorawfileparser/tests/main.nf.test.snap
+++ b/modules/bigbio/thermorawfileparser/tests/main.nf.test.snap
@@ -23,4 +23,4 @@
     },
     "timestamp": "2025-12-11T06:27:00.000000"
   }
-}
\ No newline at end of file
+}
diff --git a/modules/bigbio/thermorawfileparser/tests/nextflow.config b/modules/bigbio/thermorawfileparser/tests/nextflow.config
index 0293c16f..b4b895ea 100644
--- a/modules/bigbio/thermorawfileparser/tests/nextflow.config
+++ b/modules/bigbio/thermorawfileparser/tests/nextflow.config
@@ -1,3 +1,4 @@
 process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 }
+

From 6d04641d7354cd484709341d6913fb8f43a3fedd Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 27 Dec 2025 19:10:29 +0800
Subject: [PATCH 09/11] test

---
 modules/bigbio/thermorawfileparser/main.nf               | 1 -
 modules/bigbio/thermorawfileparser/tests/main.nf.test    | 3 +--
 modules/bigbio/thermorawfileparser/tests/nextflow.config | 1 -
 3 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/modules/bigbio/thermorawfileparser/main.nf b/modules/bigbio/thermorawfileparser/main.nf
index 5004530a..31ce4d0b 100644
--- a/modules/bigbio/thermorawfileparser/main.nf
+++ b/modules/bigbio/thermorawfileparser/main.nf
@@ -65,4 +65,3 @@ process THERMORAWFILEPARSER {
     END_VERSIONS
     """
 }
-
diff --git a/modules/bigbio/thermorawfileparser/tests/main.nf.test b/modules/bigbio/thermorawfileparser/tests/main.nf.test
index 1646f737..63e38ab9 100644
--- a/modules/bigbio/thermorawfileparser/tests/main.nf.test
+++ b/modules/bigbio/thermorawfileparser/tests/main.nf.test
@@ -50,5 +50,4 @@ nextflow_process {
             assert process.out.log.size() == 1
         }
     }
-}
-
+}
\ No newline at end of file
diff --git a/modules/bigbio/thermorawfileparser/tests/nextflow.config b/modules/bigbio/thermorawfileparser/tests/nextflow.config
index b4b895ea..0293c16f 100644
--- a/modules/bigbio/thermorawfileparser/tests/nextflow.config
+++ b/modules/bigbio/thermorawfileparser/tests/nextflow.config
@@ -1,4 +1,3 @@
 process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 }
-

From 6d591dcb051d9296f5f49b6f697f107784ab71f3 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 27 Dec 2025 19:15:49 +0800
Subject: [PATCH 10/11] Update main.nf.test

---
 modules/bigbio/thermorawfileparser/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/bigbio/thermorawfileparser/tests/main.nf.test b/modules/bigbio/thermorawfileparser/tests/main.nf.test
index 63e38ab9..355fbb15 100644
--- a/modules/bigbio/thermorawfileparser/tests/main.nf.test
+++ b/modules/bigbio/thermorawfileparser/tests/main.nf.test
@@ -50,4 +50,4 @@ nextflow_process {
             assert process.out.log.size() == 1
         }
     }
-}
\ No newline at end of file
+}

From a85d38c76a4d2f2df48b18200ad9ab0b061bb023 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 27 Dec 2025 19:22:47 +0800
Subject: [PATCH 11/11] Update modules.json

---
 modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index 5c371b97..2adc3056 100644
--- a/modules.json
+++ b/modules.json
@@ -42,7 +42,7 @@
                 "bigbio": {
                     "thermorawfileparser": {
                         "branch": "main",
-                        "git_sha": "57e0bbeaef79f0aaecad6848e334859f39ac268a",
+                        "git_sha": "f85bcb529b16e03e8f46374d0fde5bfaf604b676",
                         "installed_by": ["modules"]
                     }
                 }