Merge pull request #15 from bigbio/dev

u
bigbio · Aug 6, 2022 · 8342adf · 8342adf
2 parents 183588f + 4141176
commit 8342adf
Show file tree

Hide file tree

Showing 6 changed files with 681 additions and 30 deletions.
diff --git a/bin/diann_convert.py b/bin/diann_convert.py
diff --git a/conf/modules.config b/conf/modules.config
@@ -176,12 +176,13 @@ process {
 
     // IDFILTER on PROTEIN LEVEL
     level = params.protein_quant == 'strictly_unique_peptides' ? 'prot' : 'protgroup'
+    decoys_present = params.quantify_decoys ? ' ' : '-remove_decoys'
     withName: '.*:TMT:PROTEININFERENCE:IDFILTER' {
         ext.args    = [
             "-score:${level} \"$params.protein_level_fdr_cutoff\"",
             "-score:pep \"$params.psm_level_fdr_cutoff\"",
             "-delete_unreferenced_peptide_hits",
-            "-remove_decoys"
+            "${decoys_present}"
         ].join(' ').trim()
         ext.suffix  = '.consensusXML'
         publishDir  = [

diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf
@@ -2,35 +2,48 @@ process DIANNCONVERT {
     tag "$exp_design.Name"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.21" : null)
+    conda (params.enable_conda ? "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.13" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.21--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.13--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/sdrf-pipelines:0.0.21--pyhdfd78af_0"
+        container "quay.io/biocontainers/pmultiqc:0.0.13--pyhdfd78af_0"
     }
 
     input:
     path(report)
     path(exp_design)
+    path(report_pg)
+    path(report_pr)
+    val(meta)
+    path(fasta)
 
     output:
     path "*msstats_in.csv", emit: out_msstats
     path "*triqler_in.tsv", emit: out_triqler
+    path "*.mztab", emit: out_mztab
     path "versions.yml", emit: version
 
     script:
     def args = task.ext.args ?: ''
+    def dia_params = [meta.fragmentmasstolerance,meta.fragmentmasstoleranceunit,meta.precursormasstolerance,
+                        meta.precursormasstoleranceunit,meta.enzyme,meta.fixedmodifications,meta.variablemodifications].join(';')
 
     """
     diann_convert.py convert \\
-        --diann_report ${report} \\
-        --exp_design ${exp_design} \\
+        --diann_report "${report}" \\
+        --exp_design "${exp_design}" \\
+        --pg_matrix "${report_pg}" \\
+        --pr_matrix "${report_pr}" \\
+        --dia_params "${dia_params}" \\
+        --fasta "${fasta}" \\
+        --charge $params.max_precursor_charge \\
+        --missed_cleavages $params.allowed_missed_cleavages \\
         --qvalue_threshold $params.protein_level_fdr_cutoff \\
-        |& tee trans_to_msstats.log
+        |& tee convert_report.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        sdrf-pipelines: \$(echo "0.0.21")
+        pyopenms: \$(echo "2.8.0")
     END_VERSIONS
     """
 }
diff --git a/modules/local/diannconvert/meta.yml b/modules/local/diannconvert/meta.yml
@@ -1,10 +1,11 @@
 name: DIANNCONVERT
-description: A module to convert DIA report files to MSstats
+description: A module to convert DIA report files to MSstats, Triqler and mzTab
 keywords:
   - DIA-NN
   - conversion
   - MSstats
   - Triqler
+  - mzTab
 tools:
   - custom:
       description: |
@@ -20,6 +21,21 @@ input:
       type: file
       description: An experimental design file including Sample and replicates column et al.
       pattern: "*.tsv"
+  - report_pr:
+      type: file
+      description: A text table containing normalized quantities for precursors. They are filtered at 1% FDR, using both global and run-specific q-values for precursors
+      pattern: "*pr_matrix.tsv"
+  - report_pg:
+      type: file
+      description: A text table containing normalized quantities for protein groups. They are filtered at 1% FDR, using global q-values for protein groups
+      pattern: "*pg_matrix.tsv"
+  - meta:
+      type: map
+      description: Groovy Map containing sample information
+  - fasta:
+      type: file
+      description: Protein sequence database in Fasta format.
+      pattern: "*.{fasta,fa}"
 output:
   - out_msstats:
       type: file
@@ -29,9 +45,14 @@ output:
       type: file
       description: Triqler input file
       pattern: "out_triqler.tsv"
+  - out_mztab:
+      type: file
+      description: mzTab
+      pattern: "*.mztab"
   - version:
       type: file
       description: File containing software version
       pattern: "versions.yml"
 authors:
   - "@daichengxin"
+  - "@wanghong"
diff --git a/modules/local/diannsummary/main.nf b/modules/local/diannsummary/main.nf
@@ -16,6 +16,7 @@ process DIANNSUMMARY {
     path "diann_report.pr_matrix.tsv", emit: pr_matrix
     path "diann_report.pg_matrix.tsv", emit: pg_matrix
     path "diann_report.gg_matrix.tsv", emit: gg_matrix
+    path "diann_report.unique_genes_matrix.tsv", emit: unique_gene_matrix
     path "diannsummary.log", emit: log
     path "versions.yml", emit: version
 

diff --git a/workflows/dia.nf b/workflows/dia.nf
@@ -85,7 +85,8 @@ workflow DIA {
     //
     // MODULE: DIANNCONVERT
     //
-    DIANNCONVERT(DIANNSUMMARY.out.main_report, ch_expdesign)
+    DIANNCONVERT(DIANNSUMMARY.out.main_report, ch_expdesign, DIANNSUMMARY.out.pg_matrix, DIANNSUMMARY.out.pr_matrix, 
+                ch_result.meta.first(), params.database)
     ch_software_versions = ch_software_versions.mix(DIANNCONVERT.out.version.ifEmpty(null))
 
     //