Feature/update base image and command

modules/msk/facets/2.0.10/main.nf

@@ -0,0 +1,92 @@
+process FACETS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'docker://ghcr.io/mskcc-omics-workflows/facets_tools:2.0.10':
+        'ghcr.io/mskcc-omics-workflows/facets_tools:2.0.10' }"
+
+
+    input:
+
+    tuple val(meta), path(snp_pileup), val(legacy_output_mode)  //  [ meta, ${prefix}.snp_pileup.gz, false]
+
+
+    output:
+    tuple val(meta), path("*purity_diplogR.adjusted.seg")      , emit: purity_adjusted_seg
+    tuple val(meta), path("*purity_diplogR.unadjusted.seg")    , emit: purity_unadjusted_seg
+    tuple val(meta), path("*_purity.?d*")                      , emit: purity_r_data
+    tuple val(meta), path("*_purity*png")                      , emit: purity_png
+    tuple val(meta), path("*_purity.out")                      , emit: purity_out, optional: true
+    tuple val(meta), path("*_purity.cncf.txt")                 , emit: purity_cncf_txt, optional: true
+    tuple val(meta), path("*_hisens_diplogR.adjusted.seg")     , emit: hisens_adjusted_seg
+    tuple val(meta), path("*_hisens_diplogR.unadjusted.seg")   , emit: hisens_unadjusted_seg
+    tuple val(meta), path("*_hisens*png")                      , emit: hisens_png
+    tuple val(meta), path("*_hisens.out")                      , emit: hisens_out, optional: true
+    tuple val(meta), path("*_hisens.cncf.txt")                 , emit: hisens_cncf_txt, optional: true
+    tuple val(meta), path("*.qc.txt")                          , emit: qc_txt
+    tuple val(meta), path("*.gene_level.txt")                  , emit: gene_level_txt
+    tuple val(meta), path("*.arm_level.txt")                   , emit: arm_level_txt
+    tuple val(meta), path("${meta.id}.txt")                    , emit: output_txt, optional: true
+    path "versions.yml"                                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def legacy_output_arg = legacy_output_mode ? '--legacy-output TRUE' : ''
+
+    """
+    /usr/bin/facets-suite/run-facets-wrapper.R \
+        ${args} \
+        ${legacy_output_arg} \
+        --sample-id ${prefix} \
+        --counts-file ${snp_pileup}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        facets_suite: \$(Rscript -e "packageVersion('facetsSuite')" | grep -oP "\\d+.\\d+.\\d+")
+        facets: \$(Rscript -e "packageVersion('facets')" | grep -oP "\\d+.\\d+.\\d+")
+        r: \$(R --version | grep -oP '(?<=R version ).*(?=\\()')
+        pctGCdata: \$(Rscript -e "packageVersion('pctGCdata')" | grep -oP "\\d+.\\d+.\\d+")
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_purity_diplogR.adjusted.seg
+    touch ${prefix}_purity_diplogR.unadjusted.seg
+    touch ${prefix}_purity.CNCF.png
+    touch ${prefix}_purity.png
+    touch ${prefix}_purity.cncf.txt
+    touch ${prefix}_purity.Rdata
+    touch ${prefix}_purity.rds
+    touch ${prefix}_purity.out
+    touch ${prefix}_hisens_diplogR.adjusted.seg
+    touch ${prefix}_hisens_diplogR.unadjusted.seg
+    touch ${prefix}_hisens.CNCF.png
+    touch ${prefix}_hisens.png
+    touch ${prefix}_hisens.cncf.txt
+    touch ${prefix}_hisens.Rdata
+    touch ${prefix}_hisens.rds
+    touch ${prefix}_hisens.out
+    touch ${prefix}.qc.txt
+    touch ${prefix}.gene_level.txt
+    touch ${prefix}.arm_level.txt
+    touch ${prefix}.txt
+
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        facets_suite: \$(Rscript -e "packageVersion('facetsSuite')" | grep -oP "\\d+.\\d+.\\d+")
+        facets: \$(Rscript -e "packageVersion('facets')" | grep -oP "\\d+.\\d+.\\d+")
+        r: \$(R --version | grep -oP '(?<=R version ).*(?=\\()')
+        pctGCdata: \$(Rscript -e "packageVersion('pctGCdata')" | grep -oP "\\d+.\\d+.\\d+")
+    END_VERSIONS
+    """
+}

modules/msk/facets/2.0.10/meta.yml

@@ -0,0 +1,209 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "facets"
+description:
+  Algorithm to implement Fraction and Allele specific Copy number Estimate
+  from Tumor/normal Sequencing.
+keywords:
+  - facets
+  - pileup
+  - Allele specific
+  - Copy number
+tools:
+  - "facets-suite":
+      description: "An R package with functions to run"
+      homepage: "https://github.com/mskcc/facets-suite"
+      documentation: "https://github.com/mskcc/facets-suite"
+      licence: ["MIT"]
+      identifier: biotools:facets
+  - "facets":
+      description:
+        "Algorithm to implement Fraction and Allele specific Copy number
+        Estimate from Tumor/normal Sequencing."
+      homepage: "https://github.com/mskcc/facets"
+      documentation: "https://github.com/mskcc/facets"
+      doi: "10.1093/nar/gkw520"
+
+      identifier: biotools:facets
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'pair_id' ]`
+    - snp_pileup:
+        type: file
+        description: The pileup file
+        pattern: "*.snp_pileup.gz"
+    - legacy_output_mode:
+        type: boolean
+        description: Flag to run Facets in legacy output mode
+output:
+  - purity_adjusted_seg:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*purity_diplogR.adjusted.seg":
+          type: file
+          description: The purity adjusted seg file
+          pattern: "*purity_diplogR.adjusted.seg"
+  - purity_unadjusted_seg:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*purity_diplogR.unadjusted.seg":
+          type: file
+          description: The purity unadjusted seg file
+          pattern: "*purity_diplogR.unadjusted.seg"
+  - purity_r_data:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*_purity.?d*":
+          type: file
+          description: The purity R data file
+          pattern: "*_purity.?d*"
+  - purity_png:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*_purity*png":
+          type: file
+          description: The purity png file. In legacy output the file would match *.CNCF.png
+          pattern: "*_purity*png"
+  - purity_out:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*_purity.out":
+          type: file
+          description: The purity out file. Only in legacy output mode.
+          pattern: "*_purity.out"
+  - purity_cncf_txt:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*_purity.cncf.txt":
+          type: file
+          description: The purity cncf file. Only in legacy output mode.
+          pattern: "*_purity.cncf.txt"
+    - hisens_adjusted_seg:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*hisens_diplogR.adjusted.seg":
+          type: file
+        description: The hisens adjusted seg file
+        pattern: "*hisens_diplogR.adjusted.seg"
+    - hisens_unadjusted_seg:
+      - meta:
+        type: map
+        description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'pair_id' ]`
+      - "*hisens_diplogR.unadjusted.seg":
+        type: file
+        description: The hisens unadjusted seg file
+        pattern: "*hisens_diplogR.unadjusted.seg"
+  - hisens_r_data:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*_hisens.?d*":
+          type: file
+          description: The hisens R data file
+          pattern: "*_hisens.?d*"
+  - hisens_png:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*_hisens*png":
+          type: file
+          description: The hisens png file. In legacy output the file would match *.CNCF.png
+          pattern: "*_hisens*png"
+  - hisens_out:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*_hisens.out":
+          type: file
+          description: The hisense out file. Only in legacy output mode.
+          pattern: "*_hisens.out"
+  - hisens_cncf_txt:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*_hisens.cncf.txt":
+          type: file
+          description: The hisens cncf file. Only in legacy output mode.
+          pattern: "*_hisens.cncf.txt"
+  - qc_txt:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*.qc.txt":
+          type: file
+          description: The qc file
+          pattern: "*.qc.txt"
+  - gene_level_txt:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*.gene_level.txt":
+          type: file
+          description: The gene level file
+          pattern: "*.gene_level.txt"
+  - arm_level_txt:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - "*.arm_level.txt":
+          type: file
+          description: The arm level file
+          pattern: "*.arm_level.txt"
+  - output_txt:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'pair_id' ]`
+      - ${meta.id}.txt:
+          type: file
+          description: The facets output log file. Format [id].txt
+          pattern: "*.txt"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@nikhil"
+maintainers:
+  - "@nikhil"

modules/msk/facets/tests/main.nf.test → modules/msk/facets/2.0.10/tests/main.nf.test

@@ -9,13 +9,14 @@ nextflow_process {
     tag "modules_nfcore"
     tag "modules_msk"
     tag "facets"
+    tag "facets/2.0.10"
     tag "snppileup"
 
     test("facets - pileup - legacy output") {
 
         setup {
             run("SNPPILEUP"){
-                script "../../snppileup/main.nf"
+                script "../../../snppileup/main.nf"
                 process {
                     """                
                     meta = [ id:'test' ] // meta map
@@ -42,9 +43,7 @@ nextflow_process {
         when {
             process {
                 """                
-                meta = [ id:'test' ] // meta map
-                input[0] = SNPPILEUP.out.pileup.collect{ meta, pileup -> pileup }.map{ pileup -> [meta, pileup, true]}               
-
+                input[0] = SNPPILEUP.out.pileup.map{ meta1, pileup -> [meta1, pileup, true] }
                 """
 
             }
@@ -63,9 +62,9 @@ nextflow_process {
 
         setup {
             run("SNPPILEUP"){
-                script "../../snppileup/main.nf"
+                script "../../../snppileup/main.nf"
                 process {
-                    """                
+                    """
                     meta = [ id:'test' ] // meta map
                     input[0] = [
                                     meta,
@@ -89,12 +88,9 @@ nextflow_process {
 
         when {
             process {
-                """                
-                meta = [ id:'test' ] // meta map
-                input[0] = SNPPILEUP.out.pileup.collect{ meta, pileup -> pileup }.map{ pileup -> [meta, pileup, false]}               
-
                 """
-
+                input[0] = SNPPILEUP.out.pileup.map{ meta1, pileup -> [meta1, pileup, false] }
+                """
             }
         }