Set up meta.yml file and fix typos

modules/nf-core/purecn/run/main.nf

@@ -33,7 +33,7 @@ process PURECN_RUN {
     tuple val(meta), path("*_loh-effects-stats.html")          , emit: loh_effects_html
     tuple val(meta), path("*_loh-effects.vcf.gz")              , emit: loh_effects_vcf
     tuple val(meta), path("*_loh-effects.vcf.gz.tbi")          , emit: loh_effects_tbi
-    tuple val(meta), path("*_purecn-lohsummary.yaml")          , emit: loh_summary_yaml
+    tuple val(meta), path("*_loh-summary.yaml")                , emit: loh_summary_yaml
     tuple val(meta), path("*_loh-effects.csv")                 , emit: loh_effects_csv
     tuple val(meta), path("*_segmentation.pdf")                , emit: segmentation_pdf
     tuple val(meta), path("*_sort_coverage_loess.png")         , emit: sort_coverage_loess_png
@@ -96,7 +96,7 @@ process PURECN_RUN {
     touch ${prefix}_loh-effects-stats.html
     touch ${prefix}_loh-effects.vcf.gz
     touch ${prefix}_loh-effects.vcf.gz.tbi
-    touch ${prefix}_purecn-lohsummary.yaml
+    touch ${prefix}_loh-summary.yaml
     touch ${prefix}_loh-effects.csv
     touch ${prefix}_segmentation.pdf
     touch ${prefix}_sort_coverage_loess.png

modules/nf-core/purecn/run/meta.yml

@@ -1,7 +1,10 @@
-name: "purecn_run"
-description: run PureCN to normalize, segment and determine purity and ploidy
+name: "purecn run"
+description: Run PureCN workflow to normalize, segment and determine purity and ploidy
 keywords:
   - copy number alteration calling
+  - hybrid capture sequencing
+  - targeted sequencing
+  - DNA sequencing
 tools:
   - "purecn":
       description: "Copy number calling and SNV classification using targeted short read sequencing"
@@ -10,41 +13,173 @@ tools:
       tool_dev_url: "https://github.com/lima1/PureCN"
       doi: "10.1186/s13029-016-0060-z"
       licence: "Artistic-2.0"
+      args_id: "$args"
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
-  # Only when we have meta
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  #
-  ## TODO nf-core: Delete / customise this example input
-  - bam:
+        e.g. [ id:'test' ]
+  - intervals:
       type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: |
+        BED file of target intervals, generated from IntervalFile.R
+      pattern: "{*.bed,*.txt}"
+  - coverage:
+      type: file
+      description: Coverage file generated from Coverage.R
+      pattern: "*.txt"
+  - vcf:
+      type: file
+      description: |
+        Normal panel in VCF format, used to calculate mapping bias
+      pattern: "*.vcf.gz"
+  - normaldb:
+        type: file
+        description: |
+            Normal panel in RDS format, generated from NormalDB.R
+        pattern: "*.rds"
+  - genome:
+      type: string
+      description: Genome build
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
-  #Only when we have meta
-  - meta:
-      type: map
+  - csv:
+      type: file
       description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  #
+        CSV file containing copy number calls
+      pattern: "*.csv"
+  - variants_csv:
+        type: file
+        description: |
+            CSV file containing SNV calls
+        pattern: "*_variants.csv"
+  - pdf:
+        type: file
+        description: |
+            PDF file containing copy number plots
+        pattern: "*.pdf"
+  - rds:
+        type: file
+        description: |
+            RDS file containing copy number calls
+        pattern: "*.rds"
+  - amplification_pvalues_csv:
+        type: file
+        description: |
+            CSV file containing amplification p-values
+        pattern: "*_amplification_pvalues.csv"
+  - chr_pdf:
+        type: file
+        description: |
+            PDF file containing chromosome plots
+        pattern: "*_chromosomes.pdf"
+  - seg:
+        type: file
+        description: |
+            Segmentation file generated from DNAcopy.R
+        pattern: "*_dnacopy.seg"
+  - genes_csv:
+        type: file
+        description: |
+            CSV file containing gene copy number calls
+        pattern: "*_genes.csv"
+  - local_optima_pdf:
+        type: file
+        description: |
+            PDF file containing local optima plots
+        pattern: "*_local_optima.pdf"
+  - log:
+        type: file
+        description: |
+            Log file
+        pattern: "*.log"
+  - loh_vcf:
+        type: file
+        description: |
+            VCF file containing LOH calls
+        pattern: "*_loh.vcf"
+  - loh_vcf_gz:
+        type: file
+        description: |
+            GZipped VCF file containing LOH calls
+        pattern: "*_loh.vcf.gz"
+  - loh_vcf_tbi:
+        type: file
+        description: |
+            Tabix index file for LOH VCF
+        pattern: "*_loh.vcf.gz.tbi"
+  - loh_csv:
+        type: file
+        description: |
+            CSV file containing LOH calls
+        pattern: "*_loh.csv"
+  - loh_stats_csv:
+        type: file
+        description: |
+            CSV file containing LOH statistics
+        pattern: "*_loh-effects-stats.csv"
+  - loh_effects_txt:
+        type: file
+        description: |
+            TXT file containing LOH effects
+        pattern: "*_loh-effects-stats.genes.txt"
+  - loh_effects_html:
+        type: file
+        description: |
+            HTML file containing LOH effects
+        pattern: "*_loh-effects-stats.html"
+  - loh_effects_vcf:
+        type: file
+        description: |
+            VCF file containing LOH effects
+        pattern: "*_loh-effects.vcf.gz"
+  - loh_effects_tbi:
+        type: file
+        description: |
+            Tabix index file for LOH effects VCF
+        pattern: "*_loh-effects.vcf.gz.tbi"
+  - loh_summary_yaml:
+        type: file
+        description: |
+            YAML file containing LOH summary
+        pattern: "*_loh-summary.yaml"
+  - loh_effects_csv:
+        type: file
+        description: |
+            CSV file containing LOH effects
+        pattern: "*_loh-effects.csv"
+  - segmentation_pdf:
+        type: file
+        description: |
+            PDF file containing segmentation plots
+        pattern: "*_segmentation.pdf"
+  - sort_coverage_loess_png:
+        type: file
+        description: |
+            PNG file containing sort coverage loess plots
+        pattern: "*_sort-coverage-loess.png"
+  - sort_coverage_loess_qc_txt:
+        type: file
+        description: |
+            TXT file containing sort coverage loess QC
+        pattern: "*_sort-coverage-loess.qc.txt"
+  - sort_coverage_loess_txt_gz:
+        type: file
+        description: |
+            GZipped TXT file containing sort coverage loess
+        pattern: "*_sort-coverage-loess.txt.gz"
+  - sort_coverage_txt_gz:
+        type: file
+        description: |
+            GZipped TXT file containing sort coverage
+        pattern: "*_sort-coverage.txt.gz"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  ## TODO nf-core: Delete / customise this example output
-  - bam:
-      type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
 
 authors:
   - "@aldosr"
-  - "@lbeltrame"
+  - "@lbeltrame"

tests/modules/nf-core/purecn/run/test.yml

@@ -23,7 +23,7 @@
     - path: output/purecn/test_loh-effects-stats.html
     - path: output/purecn/test_loh-effects.vcf.gz
     - path: output/purecn/test_loh-effects.vcf.gz.tbi
-    - path: output/purecn/test_lohsummary.yaml
+    - path: output/purecn/test_loh-summary.yaml
     - path: output/purecn/test_loh-effects.csv
     - path: output/purecn/test_segmentation.pdf
     - path: output/purecn/test_sort_coverage_loess.png