Merge pull request #927 from maxulysse/tumor_only

Fix tumor only for freebayes

subworkflows/local/bam_variant_calling_tumor_only_all/main.nf

@@ -93,7 +93,8 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
     // FREEBAYES
     if (tools.split(',').contains('freebayes')) {
         BAM_VARIANT_CALLING_FREEBAYES(
-            cram,
+            // Remap channel to match module/subworkflow
+            cram.map{ meta, cram, crai -> [ meta, cram, crai, [], [] ] },
             // Remap channel to match module/subworkflow
             dict.map{ it -> [ [ id:'dict' ], it ] },
             fasta,

tests/config/tags.yml

@@ -2,48 +2,53 @@
 
 tumor_normal_pair:
   - conf/modules/**
+  - main.nf
   - modules/**
+  - nextflow.config
+  - nextflow_schema.json
   - subworkflows/**
+  - tests/test_tumor_normal_pair.yml
   - workflows/**
-  - nextflow_schema.json
-  - nextflow.config
-  - main.nf
 
 save_mapped_only:
   - conf/modules/**
+  - main.nf
   - modules/**
+  - nextflow.config
+  - nextflow_schema.json
   - subworkflows/**
+  - tests/test_save_mapped.yml
   - workflows/**
-  - nextflow_schema.json
-  - nextflow.config
-  - main.nf
 
 save_output_as_bam_only:
   - conf/modules/**
+  - main.nf
   - modules/**
+  - nextflow.config
+  - nextflow_schema.json
   - subworkflows/**
+  - tests/test_save_output_as_bam_only.yml
   - workflows/**
-  - nextflow_schema.json
-  - nextflow.config
-  - main.nf
 
 skip_all_qc:
   - conf/modules/**
+  - main.nf
   - modules/**
+  - nextflow.config
+  - nextflow_schema.json
   - subworkflows/**
+  - tests/test_skip_all_qc.yml
   - workflows/**
-  - nextflow_schema.json
-  - nextflow.config
-  - main.nf
 
 skip_markduplicates:
   - conf/modules/**
+  - main.nf
   - modules/**
+  - nextflow.config
+  - nextflow_schema.json
   - subworkflows/**
+  - tests/test_skip_markduplicates.yml
   - workflows/**
-  - nextflow_schema.json
-  - nextflow.config
-  - main.nf
 
 # preprocessing
 
@@ -55,6 +60,7 @@ alignment_to_fastq:
   - modules/nf-core/samtools/merge/main.nf
   - modules/nf-core/samtools/view/main.nf
   - subworkflows/local/bam_convert_samtools/main.nf
+  - tests/test_alignment_to_fastq.yml
 
 ## umi
 umi:
@@ -69,11 +75,13 @@ umi:
   - modules/nf-core/samtools/bam2fq/main.nf
   - subworkflows/local/fastq_align_bwamem_mem2_dragmap/main.nf
   - subworkflows/local/fastq_create_umi_consensus_fgbio/main.nf
+  - tests/test_umi.yml
 
 ## fastp
 fastp:
   - conf/modules/trimming.config
   - modules/nf-core/fastp/main.nf
+  - tests/test_fastp.yml
 
 ## aligner
 
@@ -82,18 +90,21 @@ bwamem:
   - conf/modules/aligner.config
   - modules/nf-core/bwa/mem/main.nf
   - subworkflows/local/fastq_align_bwamem_mem2_dragmap/main.nf
+  - tests/test_alignment_bwamem.yml
 
 ### bwamem2
 bwamem2:
   - conf/modules/aligner.config
   - modules/nf-core/bwamem2/mem/main.nf
   - subworkflows/local/fastq_align_bwamem_mem2_dragmap/main.nf
+  - tests/test_alignment_bwamem2.yml
 
 ### dragmap
 dragmap:
   - conf/modules/aligner.config
   - modules/nf-core/dragmap/align/main.nf
   - subworkflows/local/fastq_align_bwamem_mem2_dragmap/main.nf
+  - tests/test_alignment_dragmap.yml
 
 ## markduplicates
 markduplicates:
@@ -105,6 +116,8 @@ markduplicates:
   - modules/nf-core/samtools/stats/main.nf
   - subworkflows/local/bam_markduplicates/main.nf
   - subworkflows/local/cram_qc_mosdepth_samtools/main.nf
+  - tests/test_markduplicates_from_bam.yml
+  - tests/test_markduplicates_from_cram.yml
 
 ## prepare_recalibration
 prepare_recalibration:
@@ -113,6 +126,8 @@ prepare_recalibration:
   - modules/nf-core/gatk4/gatherbqsrreports/main.nf
   - modules/nf-core/samtools/convert/main.nf
   - subworkflows/local/bam_baserecalibrator/main.nf
+  - tests/test_prepare_recalibration_from_bam.yml
+  - tests/test_prepare_recalibration_from_cram.yml
 
 ## recalibrate
 recalibrate:
@@ -123,6 +138,8 @@ recalibrate:
   - modules/nf-core/samtools/merge/main.nf
   - subworkflows/local/bam_applybqsr/main.nf
   - subworkflows/local/cram_merge_index_samtools/main.nf
+  - tests/test_recalibrate_from_bam.yml
+  - tests/test_recalibrate_from_cram.yml
 
 ## intervals
 intervals:
@@ -132,6 +149,7 @@ intervals:
   - modules/nf-core/gatk4/intervallisttobed/main.nf
   - modules/nf-core/tabix/bgziptabix/main.nf
   - subworkflows/local/prepare_intervals/main.nf
+  - tests/test_intervals.yml
 
 ## gatk4_spark
 gatk4_spark:
@@ -145,6 +163,7 @@ gatk4_spark:
   - subworkflows/local/bam_applybqsr_spark/main.nf
   - subworkflows/local/bam_baserecalibrator_spark/main.nf
   - subworkflows/local/bam_markduplicates_spark/main.nf
+  - tests/test_gatk4_spark.yml
 
 # variant calling
 
@@ -156,6 +175,7 @@ cnvkit:
   - modules/nf-core/cnvkit/reference/main.nf
   - subworkflows/local/bam_variant_calling_cnvkit/main.nf
   - subworkflows/local/prepare_reference_cnvkit/main.nf
+  - tests/test_cnvkit.yml
 
 ## controlfreec
 controlfreec:
@@ -168,9 +188,10 @@ controlfreec:
   - modules/nf-core/controlfreec/freec2circos/main.nf
   - modules/nf-core/controlfreec/makegraph/main.nf
   - modules/nf-core/samtools/mpileup/main.nf
+  - subworkflows/local/bam_variant_calling_mpileup/main.nf
   - subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf
-  - subworkflows/local/bam_variant_calling_mpileup/main.nf
+  - tests/test_controlfreec.yml
 
 ## deepvariant
 deepvariant:
@@ -179,6 +200,7 @@ deepvariant:
   - modules/nf-core/gatk4/mergevcfs/main.nf
   - modules/nf-core/tabix/tabix/main.nf
   - subworkflows/local/bam_variant_calling_deepvariant/main.nf
+  - tests/test_deepvariant.yml
 
 ## freebayes
 freebayes:
@@ -188,19 +210,21 @@ freebayes:
   - modules/nf-core/gatk4/mergevcfs/main.nf
   - modules/nf-core/tabix/tabix/main.nf
   - subworkflows/local/bam_variant_calling_freebayes/main.nf
+  - tests/test_freebayes.yml
 
 ## haplotypecaller
 haplotypecaller:
   - conf/modules/haplotypecaller.config
+  - modules/nf-core/gatk4/cnnscorevariants/main.nf
+  - modules/nf-core/gatk4/filtervarianttranches/main.nf
   - modules/nf-core/gatk4/haplotypecaller/main.nf
   - modules/nf-core/gatk4/mergevcfs/main.nf
   - modules/nf-core/samtools/index/main.nf
   - modules/nf-core/samtools/merge/main.nf
-  - modules/nf-core/gatk4/cnnscorevariants/main.nf
-  - modules/nf-core/gatk4/filtervarianttranches/main.nf
   - subworkflows/local/bam_merge_index_samtools/main.nf
   - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf
   - subworkflows/local/vcf_variant_filtering_gatk/main.nf
+  - tests/test_haplotypecaller.yml
 
 haplotypecaller_skip_filter:
   - conf/modules/haplotypecaller.config
@@ -210,6 +234,7 @@ haplotypecaller_skip_filter:
   - modules/nf-core/samtools/merge/main.nf
   - subworkflows/local/bam_merge_index_samtools/main.nf
   - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf
+  - tests/test_haplotypecaller_skip_filter.yml
 
 ## joint_germline
 joint_germline:
@@ -229,6 +254,7 @@ joint_germline:
   - subworkflows/local/bam_merge_index_samtools/main.nf
   - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf
   - subworkflows/local/vcf_variant_filtering_gatk/main.nf
+  - tests/test_joint_germline.yml
 
 ## manta
 manta:
@@ -240,19 +266,22 @@ manta:
   - subworkflows/local/bam_variant_calling_germline_manta/main.nf
   - subworkflows/local/bam_variant_calling_somatic_manta/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf
+  - tests/test_manta.yml
 
 ## mpileup
 mpileup:
   - conf/modules/mpileup.config
   - modules/nf-core/cat/cat/main.nf
   - modules/nf-core/samtools/mpileup/main.nf
   - subworkflows/local/bam_variant_calling_mpileup/main.nf
+  - tests/test_mpileup.yml
 
 ## msisensorpro
 msisensorpro:
   - conf/modules/msisensorpro.config
-  - modules/nf-core/msisensorpro/scan/main.nf
   - modules/nf-core/msisensorpro/msi_somatic/main.nf
+  - modules/nf-core/msisensorpro/scan/main.nf
+  - tests/test_msisensorpro.yml
 
 ## mutect2
 mutect2:
@@ -267,6 +296,7 @@ mutect2:
   - modules/nf-core/gatk4/mutect2/main.nf
   - subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf
+  - tests/test_mutect2.yml
 
 ## strelka
 strelka:
@@ -276,6 +306,7 @@ strelka:
   - modules/nf-core/strelka/somatic/main.nf
   - subworkflows/local/bam_variant_calling_single_strelka/main.nf
   - subworkflows/local/bam_variant_calling_somatic_strelka/main.nf
+  - tests/test_strelka.yml
 
 ## strelka_bp
 strelka_bp:
@@ -286,6 +317,7 @@ strelka_bp:
   - modules/nf-core/strelka/somatic/main.nf
   - subworkflows/local/bam_variant_calling_somatic_manta/main.nf
   - subworkflows/local/bam_variant_calling_somatic_strelka/main.nf
+  - tests/test_strelka_bp.yml
 
 ## tiddit
 tiddit:
@@ -295,6 +327,7 @@ tiddit:
   - modules/nf-core/tiddit/sv/main.nf
   - subworkflows/local/bam_variant_calling_single_tiddit/main.nf
   - subworkflows/local/bam_variant_calling_somatic_tiddit/main.nf
+  - tests/test_tiddit.yml
 
 # annotate
 
@@ -307,20 +340,23 @@ merge:
   - subworkflows/local/vcf_annotate_all/main.nf
   - subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf
   - subworkflows/nf-core/vcf_annotate_snpeff/main.nf
+  - tests/test_annotation_merge.yml
 
 ## snpeff
 snpeff:
   - conf/modules/annotate.config
   - modules/nf-core/snpeff/main.nf
   - modules/nf-core/tabix/bgziptabix/main.nf
   - subworkflows/nf-core/vcf_annotate_snpeff/main.nf
+  - tests/test_annotation_snpeff.yml
 
 ## vep
 vep:
   - conf/modules/annotate.config
   - modules/nf-core/ensemblvep/main.nf
   - modules/nf-core/tabix/bgziptabix/main.nf
   - subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf
+  - tests/test_annotation_vep.yml
 
 # postprocessing
 
@@ -347,3 +383,4 @@ concatenate_vcfs:
   - subworkflows/local/bam_variant_calling_mpileup/main.nf
   - subworkflows/local/bam_variant_calling_single_strelka/main.nf
   - subworkflows/local/bam_variant_calling_single_tiddit/main.nf
+  - tests/test_concat_germline_vcfs.yml

tests/csv/3.0/fastq_tumor_only.csv

@@ -0,0 +1,2 @@
+patient,sex,status,sample,lane,fastq_1,fastq_2
+test,XX,1,test2,test_L1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz

tests/test_freebayes.yml

@@ -392,22 +392,52 @@
     # binary changes md5sums on reruns
     - path: results/freebayes
       should_exist: false
-# - name: Run variant calling on tumor_only sample with freebayes
-#   command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes
-#   tags:
-#     - freebayes
-#     - tumor_only
-#     - variant_calling
-#   files:
-#     - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz
-#     - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi
-# - name: Run variant calling on tumor_only sample with freebayes without intervals
-#   command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes --no_intervals
-#   tags:
-#     - freebayes
-#     - no_intervals
-#     - tumor_only
-#     - variant_calling
-#   files:
-#     - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz
-#     - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi
+- name: Run variant calling on tumor_only sample with freebayes
+  command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes --outdir results
+  tags:
+    - freebayes
+    - tumor_only
+    - variant_calling
+  files:
+    - path: results/csv/variantcalled.csv
+      md5sum: 5c5938a7bcc814cdaf5433c1120964c5
+    - path: results/multiqc
+    - path: results/reports/bcftools/freebayes/sample2/sample2.freebayes.bcftools_stats.txt
+    # conda changes md5sums for test
+    - path: results/reports/vcftools/freebayes/sample2/sample2.freebayes.FILTER.summary
+      md5sum: 0df3ddeec5779344b5d463347c9c6ea8
+    - path: results/reports/vcftools/freebayes/sample2/sample2.freebayes.TsTv.count
+      md5sum: b1d308ed5087361a584cb61e7b835e1e
+    - path: results/reports/vcftools/freebayes/sample2/sample2.freebayes.TsTv.qual
+    # content changes md5sums on reruns
+    - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/freebayes
+      should_exist: false
+- name: Run variant calling on tumor_only sample with freebayes without intervals
+  command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes --no_intervals --outdir results
+  tags:
+    - freebayes
+    - no_intervals
+    - tumor_only
+    - variant_calling
+  files:
+    - path: results/csv/variantcalled.csv
+      md5sum: 5c5938a7bcc814cdaf5433c1120964c5
+    - path: results/multiqc
+    - path: results/reports/bcftools/freebayes/sample2/sample2.freebayes.bcftools_stats.txt
+    # conda changes md5sums for test
+    - path: results/reports/vcftools/freebayes/sample2/sample2.freebayes.FILTER.summary
+      md5sum: ee513ecf779b6e201b8ef98f95f25aab
+    - path: results/reports/vcftools/freebayes/sample2/sample2.freebayes.TsTv.count
+      md5sum: 2dc153ad5af26c9f8aa82442bf65b4bf
+    - path: results/reports/vcftools/freebayes/sample2/sample2.freebayes.TsTv.qual
+    # content changes md5sums on reruns
+    - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/freebayes
+      should_exist: false