Merge pull request #454 from daichengxin/dev

Support for DIANN 1.9.2, output all files.
bigbio · Dec 4, 2024 · 235dbba · 235dbba
2 parents e50daae + c7d413d
commit 235dbba
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diff --git a/modules/local/diannsummary/main.nf b/modules/local/diannsummary/main.nf
@@ -20,11 +20,15 @@ process DIANNSUMMARY {
 
     output:
     path "diann_report.tsv", emit: main_report
+    path "diann_report.parquet", emit: report_parquet optional true
+    path "diann_report.protein_description.tsv", emit: protein_description optional true
+    path "diann_report.stats.tsv", emit: report_stats
     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
+
     // Different library files format are exported due to different DIA-NN versions
     path "empirical_library.tsv", emit: final_speclib optional true
     path "empirical_library.tsv.skyline.speclib", emit: skyline_speclib optional true

diff --git a/modules/local/openms/extractpsmfeatures/main.nf b/modules/local/openms/extractpsmfeatures/main.nf
@@ -22,7 +22,7 @@ process EXTRACTPSMFEATURES {
     def prefix = task.ext.prefix ?: "${meta.mzml_id}"
 
     feature = ""
-    if (params.ms2rescore && params.id_only) {
+    if (params.ms2rescore) {
         feature = "-extra \$(awk 'NR > 1 && \$1 !~ /psm_file/ {printf \"%s \", \$2}' ${extra_feat})"
     }