Add comments to subworkflows

nf-core · Oct 3, 2023 · cff9bc9 · cff9bc9
1 parent 758e8f2
commit cff9bc9
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Showing 3 changed files with 8 additions and 2 deletions.
diff --git a/subworkflows/local/map_alignment.nf b/subworkflows/local/map_alignment.nf
@@ -1,5 +1,5 @@
 /*
- * Perform the quantification of the samples when the parameter --skip_quantification is not provided
+ * Align retention times of runs to be able to quantify them.
  */
 include { OPENMS_MAPALIGNERIDENTIFICATION }                                 from '../../modules/local/openms_mapaligneridentification'
 include {

diff --git a/subworkflows/local/process_feature.nf b/subworkflows/local/process_feature.nf
@@ -1,5 +1,5 @@
 /*
- * Perform the quantification of the samples when the parameter --skip_quantification is not provided
+ * Perform the quantification by extracting the feature intensities and group runs corresponding to the same sample and condition.
  */
 
 include { OPENMS_IDMERGER }                                                 from '../../modules/local/openms_idmerger'

diff --git a/subworkflows/local/quant.nf b/subworkflows/local/quant.nf
@@ -1,3 +1,9 @@
+/*
+ * Perform the quantification of the samples when the parameter --skip_quantification is not provided
+ * This workflow splits the merged percolator output into the individual runs and filters them based on the q-value
+ * It then aligns the retention times of the runs and merges the idxml files together to use them as id_ext in featurefinder
+ * Finally, it performs the quantification and emits the consensusXML file
+ */
 include { OPENMS_IDRIPPER }                                                 from '../../modules/local/openms_idripper'
 include { OPENMS_IDSCORESWITCHER }                                          from '../../modules/local/openms_idscoreswitcher'
 include { PYOPENMS_IDFILTER }                                               from '../../modules/local/pyopenms_idfilter'