Small cleanup/fix

lehtiolab · Feb 3, 2025 · e9858ce · e9858ce
1 parent 4fec297
commit e9858ce
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Showing 6 changed files with 6 additions and 7 deletions.
diff --git a/bin/luciphor_parse.py b/bin/luciphor_parse.py
@@ -97,7 +97,6 @@ def main():
                     labileptms, stabileptms, args.searchengine)
             if not msgfpsm.has_labileptms():
                 continue
-            print(psm)
             if args.searchengine == 'sage':
                 scan = re.sub('.*scan=', '', psm[fields['SCANNR']])
             else:

diff --git a/containers.json b/containers.json
@@ -16,7 +16,7 @@
   },
   "openms": {
       "version": "3.3.0",
-      "docker": "quay.io/biocontainers/openms:openms:3.3.0--h0656172_8",
+      "docker": "quay.io/biocontainers/openms:3.3.0--h0656172_8",
       "singularity": "https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8"
   },
   "dinosaur": {

diff --git a/main.nf b/main.nf
@@ -242,7 +242,7 @@ process createNewSpectraLookup {
   container params.__containers[tag][workflow.containerEngine]
 
   input:
-  tuple val(setnames), file(mzmlfiles), val(platenames)
+  tuple val(setnames), path(mzmlfiles), val(platenames)
 
   output:
   path('target_db.sqlite')

diff --git a/modules.nf b/modules.nf
@@ -12,7 +12,7 @@ def get_field_nr_multi(fn, fieldnames) {
 }
 
 def get_complement_field_nr(fn, fieldname) {
-    /* return field nrs comma separated like: 1,2,5,9 */
+    /* return field nrs NOT matching input, comma separated like: 1,2,5,9 */
     return "\$(head -n1 ${fn} | tr '\\t' '\\n' | grep -vwn '^${fieldname}\$' | cut -f 1 -d':' | tr '\\n' ',' | sed 's/\\,\$//')"
 }
 

diff --git a/workflows/msgf_perco.nf b/workflows/msgf_perco.nf
@@ -43,7 +43,7 @@ process percolator {
   container params.__containers[tag][workflow.containerEngine]
 
   input:
-  tuple val(setname), path(mzids), path(tsvs), val(enzyme)
+  tuple val(setname), path(mzids), val(enzyme)
 
   output:
   tuple val(setname), path('perco.xml')
@@ -128,7 +128,7 @@ workflow MSGFPERCO {
   .set { mzid_tsv_2psm }
 
   mzid_tsv_2psm
-  | map {it + [enzyme] }
+  | map {[it[0], it[1], enzyme] }
   | percolator
   | join(mzid_tsv_2psm)
   | map { it + [psmconflvl, pepconflvl, output_unfilt_psms] }

diff --git a/workflows/sage_perco.nf b/workflows/sage_perco.nf
@@ -1,4 +1,4 @@
-include { createMods; listify; get_field_nr; stripchars_infile; parse_isotype } from '../modules.nf'
+include { createMods; listify; stripchars_infile; parse_isotype } from '../modules.nf'
 
 
 process sagePrepare {