Merge pull request #297 from MaxUlysse/dsl2_somatic

Add somatic to DSL2
nf-core · Jan 27, 2021 · 2a15600 · 2a15600
2 parents 8a7cb68 + daae20f
commit 2a15600
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Showing 17 changed files with 613 additions and 305 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -34,6 +34,8 @@ jobs:
       - name: Run pipeline with test data
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+      - name: Show results
+        run: ls -lR results
 
   aligner:
     name: Run aligner tests
@@ -54,6 +56,8 @@ jobs:
           NXF_VER: '20.11.0-edge'
       - name: Run ${{ matrix.profile }} test
         run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }}
+      - name: Show results
+        run: ls -lR results
 
   germline:
     name: Run input from a folder test and restart from step tests
@@ -76,12 +80,20 @@ jobs:
         run: git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
       - name: Run germline test with ${{ matrix.markduplicates }} --step mapping
         run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input data/testdata/tiny/normal --save_bam_mapped
+      - name: Show results
+        run: ls -lR results
       - name: Run germline test with ${{ matrix.markduplicates }} --step prepare_recalibration
         run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input=false --step prepare_recalibration -resume
+      - name: Show results
+        run: ls -lR results
       - name: Run germline test with ${{ matrix.markduplicates }} --step recalibrate
         run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input=false --step recalibrate -resume
+      - name: Show results
+        run: ls -lR results
       - name: Run germline test with ${{ matrix.markduplicates }} --step variantCalling
         run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input=false --step variantCalling
+      - name: Show results
+        run: ls -lR results
 
   # annotation:
   #   env:
@@ -126,24 +138,27 @@ jobs:
   #     - name: Run test for minimal genomes
   #       run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skipQC all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes
 
-  # profile:
-  #   env:
-  #     NXF_ANSI_LOG: false
-  #   runs-on: ubuntu-latest
-  #   strategy:
-  #     matrix:
-  #       profile: [test_split_fastq, test_targeted, test_trimming, test_no_gatk_spark, test_umi_tso, test_umi_qiaseq]
-  #   steps:
-  #     - uses: actions/checkout@v2
-  #     - name: Install Nextflow
-  #       run: |
-  #         wget -qO- get.nextflow.io | bash
-  #         sudo mv nextflow /usr/local/bin/
-  #       env:
-  #         # Only check Nextflow pipeline minimum version
-  #         NXF_VER: '20.11.0-edge'
-  #     - name: Run ${{ matrix.profile }} test
-  #       run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker
+  profile:
+    env:
+      NXF_ANSI_LOG: false
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # profile: [test_split_fastq, test_targeted, test_trimming, test_use_gatk_spark, test_umi_tso, test_umi_qiaseq]
+        profile: [test_use_gatk_spark, test_targeted]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+        env:
+          # Only check Nextflow pipeline minimum version
+          NXF_VER: '20.11.0-edge'
+      - name: Run ${{ matrix.profile }} test
+        run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker
+      - name: Show results
+        run: ls -lR results
 
   tools:
     name: Run tool tests
@@ -153,13 +168,13 @@ jobs:
     strategy:
       matrix:
         # tool: [Haplotypecaller, Freebayes, Manta, mpileup, MSIsensor, Strelka, TIDDIT]
-        tool: [Haplotypecaller, Strelka]
+        tool: [Haplotypecaller, Manta, MSIsensor, Strelka]
         intervals: [--no_intervals, '']
         exclude:
-        #   - tool: Manta
-        #     intervals: --no_intervals
-        #   - tool: MSIsensor
-        #     intervals: --no_intervals
+          - tool: Manta
+            intervals: --no_intervals
+          - tool: MSIsensor
+            intervals: --no_intervals
           - tool: Strelka
             intervals: --no_intervals
         #   - tool: TIDDIT
@@ -175,3 +190,5 @@ jobs:
           NXF_VER: '20.11.0-edge'
       - name: Run ${{ matrix.tool }} test
         run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}
+      - name: Show results
+        run: ls -lR results
diff --git a/conf/modules.config b/conf/modules.config
@@ -27,6 +27,14 @@ params {
             publish_dir      = "reference"
             publish_files    = "false"
         }
+        'index_target_bed' {
+            publish_dir      = "reference"
+            publish_files    = "false"
+        }
+        'msisensor_scan' {
+            publish_dir      = "reference"
+            publish_files    = "false"
+        }
         'samtools_faidx' {
             publish_dir      = "reference"
             publish_files    = "false"
@@ -144,6 +152,29 @@ params {
             publish_dir      = "variant_calling"
             publish_files    = ['vcf.gz':'strelka', 'vcf.gz.tbi':'strelka']
         }
+// TUMOR_VARIANT_CALLING
+
+// PAIR_VARIANT_CALLING
+        'manta_somatic' {
+            publish_by_id    = "true"
+            publish_dir      = "variant_calling"
+            publish_files    = ['vcf.gz':'manta', 'vcf.gz.tbi':'manta']
+        }
+        'msisensor_msi' {
+            publish_by_id    = "true"
+            publish_dir      = "variant_calling"
+            publish_files    = ['list':'msisensor']
+        }
+        'strelka_somatic' {
+            publish_by_id    = "true"
+            publish_dir      = "variant_calling"
+            publish_files    = ['vcf.gz':'strelka', 'vcf.gz.tbi':'strelka']
+        }
+        'strelka_somatic_bp' {
+            publish_by_id    = "true"
+            publish_dir      = "variant_calling"
+            publish_files    = ['vcf.gz':'strelka', 'vcf.gz.tbi':'strelka']
+        }
 // QC_TRIM
         'fastqc' {
             args             = "--quiet"

diff --git a/lib/Completion.groovy b/lib/Completion.groovy
@@ -3,7 +3,7 @@
  */
 
 class Completion {
-    static void email(workflow, params, summary, run_name, baseDir, multiqc_report, log) {
+    static void email(workflow, params, summary, run_name, projectDir, multiqc_report, log) {
 
         // Set up the e-mail variables
         def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
@@ -56,18 +56,18 @@ class Completion {
 
         // Render the TXT template
         def engine = new groovy.text.GStringTemplateEngine()
-        def tf = new File("$baseDir/assets/email_template.txt")
+        def tf = new File("$projectDir/assets/email_template.txt")
         def txt_template = engine.createTemplate(tf).make(email_fields)
         def email_txt = txt_template.toString()
 
         // Render the HTML template
-        def hf = new File("$baseDir/assets/email_template.html")
+        def hf = new File("$projectDir/assets/email_template.html")
         def html_template = engine.createTemplate(hf).make(email_fields)
         def email_html = html_template.toString()
 
         // Render the sendmail template
-        def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ]
-        def sf = new File("$baseDir/assets/sendmail_template.txt")
+        def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ]
+        def sf = new File("$projectDir/assets/sendmail_template.txt")
         def sendmail_template = engine.createTemplate(sf).make(smail_fields)
         def sendmail_html = sendmail_template.toString()
 

diff --git a/lib/Schema.groovy b/lib/Schema.groovy
@@ -108,7 +108,7 @@ class JSON {
 
         summary['MarkDuplicates'] = "Options"
         summary['Java options'] = params.markdup_java_options
-        summary['GATK Spark']   = params.no_gatk_spark ? 'No' : 'Yes'
+        summary['GATK Spark']   = params.use_gatk_spark ? 'Yes' : 'No'
 
         summary['Save BAMs mapped']   = params.save_bam_mapped ? 'Yes' : 'No'
         summary['Skip MarkDuplicates']   = params.skip_markduplicates ? 'Yes' : 'No'
@@ -126,7 +126,7 @@ class JSON {
             if (params.cf_ploidy)    summary['ploidy']             = params.cf_ploidy
         }
 
-        if ('haplotypecaller' in tools)             summary['GVCF']       = params.no_gvcf ? 'No' : 'Yes'
+        if ('haplotypecaller' in tools)             summary['GVCF']       = params.generate_gvcf ? 'Yes' : 'No'
         if ('strelka' in tools && 'manta' in tools) summary['Strelka BP'] = params.no_strelka_bp ? 'No' : 'Yes'
         if (params.pon && ('mutect2' in tools || (params.sentieon && 'tnscope' in tools))) summary['Panel of normals'] = params.pon