bigbio · ypriverol · May 27, 2025 · May 21, 2025 · May 21, 2025 · May 21, 2025
diff --git a/.../local/assemble_empirical_library/main.nf → .../diann/assemble_empirical_library/main.nf b/.../local/assemble_empirical_library/main.nf → .../diann/assemble_empirical_library/main.nf
@@ -1,4 +1,4 @@
-process ASSEMBLE_EMPIRICAL_LIBRARY {
+process DIANN_ASSEMBLE_EMPIRICAL_LIBRARY {
     tag "$meta.experiment_id"
     label 'process_low'
     label 'diann'

diff --git a/...local/assemble_empirical_library/meta.yml → ...diann/assemble_empirical_library/meta.yml b/...local/assemble_empirical_library/meta.yml → ...diann/assemble_empirical_library/meta.yml
diff --git a/modules/local/diannconvert/main.nf → modules/local/diann/convert/main.nf b/modules/local/diannconvert/main.nf → modules/local/diann/convert/main.nf
@@ -1,4 +1,4 @@
-process DIANNCONVERT {
+process DIANN_CONVERT {
     tag "$meta.experiment_id"
     label 'process_medium'
 

diff --git a/modules/local/diannconvert/meta.yml → modules/local/diann/convert/meta.yml b/modules/local/diannconvert/meta.yml → modules/local/diann/convert/meta.yml
@@ -1,4 +1,4 @@
-name: DIANNCONVERT
+name: diannconvert
 description: A module to convert DIA report files to MSstats, Triqler and mzTab
 keywords:
   - DIA-NN

diff --git a/modules/local/generate_diann_cfg/main.nf → modules/local/diann/generate_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf → modules/local/diann/generate_cfg/main.nf
@@ -1,4 +1,4 @@
-process GENERATE_DIANN_CFG {
+process DIANN_GENERATE_CFG {
     tag "$meta.experiment_id"
     label 'process_tiny'
 

diff --git a/modules/local/generate_diann_cfg/meta.yml → modules/local/diann/generate_cfg/meta.yml b/modules/local/generate_diann_cfg/meta.yml → modules/local/diann/generate_cfg/meta.yml
diff --git a/...s/local/individual_final_analysis/main.nf → ...l/diann/individual_final_analysis/main.nf b/...s/local/individual_final_analysis/main.nf → ...l/diann/individual_final_analysis/main.nf
diff --git a/.../local/individual_final_analysis/meta.yml → .../diann/individual_final_analysis/meta.yml b/.../local/individual_final_analysis/meta.yml → .../diann/individual_final_analysis/meta.yml
diff --git a/...les/local/silicolibrarygeneration/main.nf → ...diann/insilico_library_generation/main.nf b/...les/local/silicolibrarygeneration/main.nf → ...diann/insilico_library_generation/main.nf
@@ -1,4 +1,4 @@
-process SILICOLIBRARYGENERATION {
+process DIANN_INSILICO_LIBRARY_GENERATION {
     tag "$fasta.Name"
     label 'process_medium'
     label 'diann'

diff --git a/...es/local/silicolibrarygeneration/meta.yml → ...iann/insilico_library_generation/meta.yml b/...es/local/silicolibrarygeneration/meta.yml → ...iann/insilico_library_generation/meta.yml
diff --git a/.../local/diann_preliminary_analysis/main.nf → .../local/diann/preliminary_analysis/main.nf b/.../local/diann_preliminary_analysis/main.nf → .../local/diann/preliminary_analysis/main.nf
diff --git a/...local/diann_preliminary_analysis/meta.yml → ...local/diann/preliminary_analysis/meta.yml b/...local/diann_preliminary_analysis/meta.yml → ...local/diann/preliminary_analysis/meta.yml
diff --git a/modules/local/diannsummary/main.nf → modules/local/diann/summary/main.nf b/modules/local/diannsummary/main.nf → modules/local/diann/summary/main.nf
@@ -1,4 +1,4 @@
-process DIANNSUMMARY {
+process DIANN_SUMMARY {
     tag "$meta.experiment_id"
     label 'process_high'
     label 'diann'

diff --git a/modules/local/diannsummary/meta.yml → modules/local/diann/summary/meta.yml b/modules/local/diannsummary/meta.yml → modules/local/diann/summary/meta.yml
diff --git a/modules/local/msstats/main.nf → modules/local/msstats/msstats_lfq/main.nf b/modules/local/msstats/main.nf → modules/local/msstats/msstats_lfq/main.nf
@@ -1,4 +1,4 @@
-process MSSTATS {
+process MSSTATS_LFQ {
     tag "$msstats_csv_input.Name"
     label 'process_medium'
 

diff --git a/modules/local/msstats/meta.yml → modules/local/msstats/msstats_lfq/meta.yml b/modules/local/msstats/meta.yml → modules/local/msstats/msstats_lfq/meta.yml
@@ -1,4 +1,4 @@
-name: MSSTATS
+name: MSSTATS_LFQ
 description: A module to performance proteomics statistical analysis using MSstats tool.
 keywords:
   - MSstats

diff --git a/modules/local/msstatstmt/main.nf → modules/local/msstats/msstats_tmt/main.nf b/modules/local/msstatstmt/main.nf → modules/local/msstats/msstats_tmt/main.nf
@@ -1,4 +1,4 @@
-process MSSTATSTMT {
+process MSSTATS_TMT {
     tag "$msstatstmt_csv_input.Name"
     label 'process_medium'
 

diff --git a/modules/local/msstatstmt/meta.yml → modules/local/msstats/msstats_tmt/meta.yml b/modules/local/msstatstmt/meta.yml → modules/local/msstats/msstats_tmt/meta.yml
@@ -1,4 +1,4 @@
-name: MSSTATSTMT
+name: MSSTATS_TMT
 description: |
   A module to performance proteomics statistical analysis with tandem mass tag (TMT) labeling using MSstatsTMT tool.
   - MSstatsTMT

diff --git a/modules/local/decompress_dotd/main.nf → modules/local/utils/decompress_dotd/main.nf b/modules/local/decompress_dotd/main.nf → modules/local/utils/decompress_dotd/main.nf
diff --git a/modules/local/decompress_dotd/meta.yml → modules/local/utils/decompress_dotd/meta.yml b/modules/local/decompress_dotd/meta.yml → modules/local/utils/decompress_dotd/meta.yml
diff --git a/modules/local/extract_psm/main.nf → modules/local/utils/extract_psm/main.nf b/modules/local/extract_psm/main.nf → modules/local/utils/extract_psm/main.nf
diff --git a/modules/local/extract_psm/meta.yml → modules/local/utils/extract_psm/meta.yml b/modules/local/extract_psm/meta.yml → modules/local/utils/extract_psm/meta.yml
diff --git a/modules/local/extract_sample/main.nf → modules/local/utils/extract_sample/main.nf b/modules/local/extract_sample/main.nf → modules/local/utils/extract_sample/main.nf
diff --git a/modules/local/extract_sample/meta.yml → modules/local/utils/extract_sample/meta.yml b/modules/local/extract_sample/meta.yml → modules/local/utils/extract_sample/meta.yml
diff --git a/modules/local/ms2rescore/main.nf → modules/local/utils/ms2rescore/main.nf b/modules/local/ms2rescore/main.nf → modules/local/utils/ms2rescore/main.nf
diff --git a/modules/local/ms2rescore/meta.yml → modules/local/utils/ms2rescore/meta.yml b/modules/local/ms2rescore/meta.yml → modules/local/utils/ms2rescore/meta.yml
diff --git a/modules/local/mzmlstatistics/main.nf → modules/local/utils/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf → modules/local/utils/mzmlstatistics/main.nf
diff --git a/modules/local/mzmlstatistics/meta.yml → modules/local/utils/mzmlstatistics/meta.yml b/modules/local/mzmlstatistics/meta.yml → modules/local/utils/mzmlstatistics/meta.yml
diff --git a/modules/local/psm_clean/main.nf → modules/local/utils/psm_clean/main.nf b/modules/local/psm_clean/main.nf → modules/local/utils/psm_clean/main.nf
diff --git a/modules/local/psm_clean/meta.yml → modules/local/utils/psm_clean/meta.yml b/modules/local/psm_clean/meta.yml → modules/local/utils/psm_clean/meta.yml
diff --git a/modules/local/spectrum2features/main.nf → ...les/local/utils/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf → ...les/local/utils/spectrum2features/main.nf
diff --git a/modules/local/spectrum2features/meta.yml → ...es/local/utils/spectrum2features/meta.yml b/modules/local/spectrum2features/meta.yml → ...es/local/utils/spectrum2features/meta.yml
diff --git a/modules/local/tdf2mzml/main.nf → modules/local/utils/tdf2mzml/main.nf b/modules/local/tdf2mzml/main.nf → modules/local/utils/tdf2mzml/main.nf
diff --git a/modules/local/tdf2mzml/meta.yml → modules/local/utils/tdf2mzml/meta.yml b/modules/local/tdf2mzml/meta.yml → modules/local/utils/tdf2mzml/meta.yml
diff --git a/modules/local/thermorawfileparser/main.nf → ...s/local/utils/thermorawfileparser/main.nf b/modules/local/thermorawfileparser/main.nf → ...s/local/utils/thermorawfileparser/main.nf
diff --git a/modules/local/thermorawfileparser/meta.yml → .../local/utils/thermorawfileparser/meta.yml b/modules/local/thermorawfileparser/meta.yml → .../local/utils/thermorawfileparser/meta.yml
diff --git a/workflows/dia.nf b/workflows/dia.nf
@@ -7,14 +7,14 @@
 //
 // MODULES: Local to the pipeline
 //
-include { GENERATE_DIANN_CFG as DIANNCFG } from '../modules/local/generate_diann_cfg/main'
-include { DIANNCONVERT                   } from '../modules/local/diannconvert/main'
-include { MSSTATS                        } from '../modules/local/msstats/main'
-include { DIANN_PRELIMINARY_ANALYSIS     } from '../modules/local/diann_preliminary_analysis/main'
-include { ASSEMBLE_EMPIRICAL_LIBRARY     } from '../modules/local/assemble_empirical_library/main'
-include { SILICOLIBRARYGENERATION        } from '../modules/local/silicolibrarygeneration/main'
-include { INDIVIDUAL_FINAL_ANALYSIS      } from '../modules/local/individual_final_analysis/main'
-include { DIANNSUMMARY                   } from '../modules/local/diannsummary/main'
+include { DIANN_GENERATE_CFG as DIANNCFG } from '../modules/local/diann/generate_cfg/main'
+include { DIANN_CONVERT as DIANNCONVERT  } from '../modules/local/diann/convert/main'
+include { MSSTATS_LFQ as MSSTATS         } from '../modules/local/msstats/msstats_lfq/main'
+include { DIANN_PRELIMINARY_ANALYSIS     } from '../modules/local/diann/preliminary_analysis/main'
+include { DIANN_ASSEMBLE_EMPIRICAL_LIBRARY as ASSEMBLE_EMPIRICAL_LIBRARY } from '../modules/local/diann/assemble_empirical_library/main'
+include { DIANN_INSILICO_LIBRARY_GENERATION as SILICOLIBRARYGENERATION } from '../modules/local/diann/insilico_library_generation/main'
+include { INDIVIDUAL_FINAL_ANALYSIS      } from '../modules/local/diann/individual_final_analysis/main'
+include { DIANN_SUMMARY as DIANNSUMMARY  } from '../modules/local/diann/summary/main'
 
 //
 // SUBWORKFLOWS: Consisting of a mix of local and nf-core/modules

diff --git a/workflows/lfq.nf b/workflows/lfq.nf
@@ -8,7 +8,7 @@
 // MODULES: Local to the pipeline
 //
 include { PROTEOMICSLFQ } from '../modules/local/openms/proteomicslfq/main'
-include { MSSTATS       } from '../modules/local/msstats/main'
+include { MSSTATS_LFQ as MSSTATS } from '../modules/local/msstats/msstats_lfq/main'
 
 //
 // SUBWORKFLOWS: Consisting of a mix of local and nf-core/modules

diff --git a/workflows/tmt.nf b/workflows/tmt.nf
@@ -8,7 +8,7 @@
 // MODULES: Local to the pipeline
 //
 include { FILEMERGE  } from '../modules/local/openms/filemerge/main'
-include { MSSTATSTMT } from '../modules/local/msstatstmt/main'
+include { MSSTATS_TMT as MSSTATSTMT } from '../modules/local/msstats/msstats_tmt/main'
 
 //
 // SUBWORKFLOWS: Consisting of a mix of local and nf-core/modules