Merge pull request #203 from bigbio/patch-pmultiqc-0.0.12

Update main.nf

Author: ypriverol

modules/local/pmultiqc/main.nf

@@ -1,11 +1,11 @@
 process PMULTIQC {
     label 'process_high'
 
-    conda (params.enable_conda ? "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.11" : null)
+    conda (params.enable_conda ? "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.11--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.12--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/pmultiqc:0.0.11--pyhdfd78af_0"
+        container "quay.io/biocontainers/pmultiqc:0.0.12--pyhdfd78af_0"
     }
 
     input:

workflows/dia.nf

@@ -100,7 +100,7 @@ workflow DIA {
     emit:
     versions        = ch_software_versions
     diann_report    = DIANNSUMMARY.out.main_report
-    msstats_csv     = DIANNCONVERT.out.out_msstats
+    msstats_in      = DIANNCONVERT.out.out_msstats
     out_triqler     = DIANNCONVERT.out.out_triqler
     msstats_out     = ch_msstats_out
 

workflows/lfq.nf

@@ -75,6 +75,7 @@ workflow LFQ {
     ch_pmultiqc_ids = ch_pmultiqc_ids
     final_result    = PROTEOMICSLFQ.out.out_mztab
     versions        = ch_software_versions
+    msstats_in      = PROTEOMICSLFQ.out.out_msstats
     msstats_out     = ch_msstats_out
 }
 

workflows/quantms.nf

@@ -116,6 +116,7 @@ workflow QUANTMS {
     //
     ch_pipeline_results = Channel.empty()
     ch_ids_pmultiqc = Channel.empty()
+    ch_msstats_in = Channel.empty()
 
     //
     // MODULE: Generate decoy database
@@ -141,15 +142,18 @@ workflow QUANTMS {
     TMT(ch_fileprep_result.iso, CREATE_INPUT_CHANNEL.out.ch_expdesign, ch_searchengine_in_db)
     ch_ids_pmultiqc = ch_ids_pmultiqc.mix(TMT.out.ch_pmultiqc_ids)
     ch_pipeline_results = ch_pipeline_results.mix(TMT.out.final_result)
+    ch_msstats_in = ch_msstats_in.mix(TMT.out.msstats_in)
     ch_versions = ch_versions.mix(TMT.out.versions.ifEmpty(null))
 
     LFQ(ch_fileprep_result.lfq, CREATE_INPUT_CHANNEL.out.ch_expdesign, ch_searchengine_in_db)
     ch_ids_pmultiqc = ch_ids_pmultiqc.mix(LFQ.out.ch_pmultiqc_ids)
     ch_pipeline_results = ch_pipeline_results.mix(LFQ.out.final_result)
+    ch_msstats_in = ch_msstats_in.mix(LFQ.out.msstats_in)
     ch_versions = ch_versions.mix(LFQ.out.versions.ifEmpty(null))
 
     DIA(ch_fileprep_result.dia, CREATE_INPUT_CHANNEL.out.ch_expdesign)
     ch_pipeline_results = ch_pipeline_results.mix(DIA.out.diann_report)
+    ch_msstats_in = ch_msstats_in.mix(DIA.out.msstats_in)
     ch_versions = ch_versions.mix(DIA.out.versions.ifEmpty(null))
 
 
@@ -177,7 +181,8 @@ workflow QUANTMS {
         CREATE_INPUT_CHANNEL.out.ch_expdesign
             .combine(ch_pipeline_results.ifEmpty([]).combine(ch_multiqc_files.collect())
             .combine(ch_pmultiqc_mzmls.collect())
-            .combine(ch_ids_pmultiqc.collect().ifEmpty([]))),
+            .combine(ch_ids_pmultiqc.collect().ifEmpty([])))
+            .combine(ch_msstats_in),
         ch_multiqc_quantms_logo
     )
     multiqc_report      = SUMMARYPIPELINE.out.ch_pmultiqc_report.toList()

workflows/tmt.nf

@@ -83,7 +83,7 @@ workflow TMT {
     emit:
     ch_pmultiqc_ids = ch_pmultiqc_ids
     final_result    = PROTEINQUANT.out.out_mztab
-    msstats_input   = PROTEINQUANT.out.msstats_csv
+    msstats_in  = PROTEINQUANT.out.msstats_csv
     msstats_out     = ch_msstats_out
     versions        = ch_software_versions
 }