Fix design and tag renaming changes

bigbio · May 5, 2022 · 8361c38 · 8361c38
1 parent bfd1389
commit 8361c38
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Showing 4 changed files with 20 additions and 15 deletions.
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -15,3 +15,7 @@ export_plots: true
 custom_logo: "./nf-core-quantms_logo_light.png"
 custom_logo_url: "https://github.com/bigbio/quantms"
 custom_logo_title: "quantms"
+
+sp:
+  quantms/exp_design:
+    fn: "*_design.tsv"
diff --git a/modules/local/openms/proteomicslfq/main.nf b/modules/local/openms/proteomicslfq/main.nf
@@ -1,5 +1,5 @@
 process PROTEOMICSLFQ {
-    tag "$expdes.Name"
+    tag "${expdes.baseName - ~/_design$/}"
     label 'process_high'
 
     conda (params.enable_conda ? "bioconda::openms=2.8.0" : null)
@@ -14,8 +14,8 @@ process PROTEOMICSLFQ {
     path(fasta)
 
     output:
-    path "${expdes.baseName}.mzTab", emit: out_mztab
-    path "${expdes.baseName}.consensusXML", emit: out_consensusXML
+    path "${expdes.baseName - ~/_design$/}.mzTab", emit: out_mztab
+    path "${expdes.baseName - ~/_design$/}.consensusXML", emit: out_consensusXML
     path "*out_msstats.csv", emit: out_msstats optional true
     path "*out_triqler.tsv", emit: out_triqler optional true
     path "debug_mergedIDs.idXML", emit: debug_mergedIDs optional true
@@ -29,8 +29,8 @@ process PROTEOMICSLFQ {
 
     script:
     def args = task.ext.args ?: ''
-    def msstats_present = params.quantification_method == "feature_intensity" ? "-out_msstats ${expdes.baseName}_msstats_in.csv" : ""
-    def triqler_present = (params.quantification_method == "feature_intensity") && (params.add_triqler_output) ? "-out_triqler ${expdes.baseName}_triqler_in.tsv" : ""
+    def msstats_present = params.quantification_method == "feature_intensity" ? "-out_msstats ${expdes.baseName - ~/_design$/}_msstats_in.csv" : ""
+    def triqler_present = (params.quantification_method == "feature_intensity") && (params.add_triqler_output) ? "-out_triqler ${expdes.baseName - ~/_design$/}_triqler_in.tsv" : ""
     def decoys_present = (params.quantify_decoys || ((params.quantification_method == "feature_intensity") && params.add_triqler_output)) ? '-PeptideQuantification:quantify_decoys' : ''
 
     """
@@ -47,12 +47,12 @@ process PROTEOMICSLFQ {
         -protein_quantification ${params.protein_quant} \\
         -alignment_order ${params.alignment_order} \\
         -picked_proteinFDR true \\
-        -out ${expdes.baseName}.mzTab \\
+        -out ${expdes.baseName - ~/_design$/}.mzTab \\
         -threads ${task.cpus} \\
         ${msstats_present} \\
         ${triqler_present} \\
         ${decoys_present} \\
-        -out_cxml out.consensusXML \\
+        -out_cxml ${expdes.baseName - ~/_design$/}.consensusXML \\
         -proteinFDR ${params.protein_level_fdr_cutoff} \\
         $args \\
         |& tee proteomicslfq.log

diff --git a/modules/local/pmultiqc/main.nf b/modules/local/pmultiqc/main.nf
@@ -14,14 +14,14 @@ process PMULTIQC {
 
     output:
     path "*.html", emit: ch_pmultiqc_report
-    path "*.db", optional:true, emit: ch_pmultiqc_db
+    path "*.db", optional: true, emit: ch_pmultiqc_db
     path "versions.yml", emit: versions
     path "*_data", emit: data
-    path "*_plots", optional:true, emit: plots
+    path "*_plots", optional: true, emit: plots
 
     script:
     def args = task.ext.args ?: ''
-    def disable_pmultqic = params.enable_pmultiqc ? "": "--disable_plugin"
+    def disable_pmultqic = params.enable_pmultiqc ? "" : "--disable_plugin"
 
     """
     multiqc \\

diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf
@@ -5,24 +5,25 @@
 process PREPROCESS_EXPDESIGN {
     label 'process_very_low'
     label 'process_single_thread'
+    tag "$design.Name"
 
     container "frolvlad/alpine-bash"
 
     input:
-    path design, stageAs: '${design.baseName}_raw.tsv'
+    path design
 
     output:
-    path "experimental_design.tsv", emit: ch_expdesign
-    path "config.tsv", emit: ch_config
+    path "${design.baseName}_design.tsv", emit: ch_expdesign
+    path "${design.baseName}_config.tsv", emit: ch_config
 
     script:
 
     """
     # since we know that we will need to convert from raw to mzML for all tools that need the design (i.e., OpenMS tools)
     # we edit the design here and change the endings.
-    sed 's/.raw\\t/.mzML\\t/I' ${design.baseName}_raw.tsv > ${design.baseName}.tsv
+    sed 's/.raw\\t/.mzML\\t/I' ${design} > ${design.baseName}_design.tsv
 
     # here we extract the filenames and fake an empty config (since the config values will be deduced from the workflow params)
-    a=\$(grep -n '^\$' ${design.baseName}_raw.tsv | head -n1| awk -F":" '{print \$1}'); sed -e ''"\${a}"',\$d' ${design.baseName}_raw.tsv > ${design.baseName}_config.tsv
+    a=\$(grep -n '^\$' ${design} | head -n1| awk -F":" '{print \$1}'); sed -e ''"\${a}"',\$d' ${design} > ${design.baseName}_config.tsv
     """
 }