FIX: Better coverage for all tests

CHANGELOG.md

@@ -64,6 +64,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
 - [#1216](https://github.com/nf-core/sarek/pull/1216) - Better test coverage for variant calling `*_all` subworkflows
 - [#1217](https://github.com/nf-core/sarek/pull/1217) - Fix `groupTuple` statement for mutect2 tumor_only subworkflows
 - [#1220](https://github.com/nf-core/sarek/pull/1220) - Fix channel and meta logic for `joint_mutect2` feature
+- [#1225](https://github.com/nf-core/sarek/pull/1225) - Better test coverage for all tests
 
 ### Dependencies
 

tests/config/tags.yml

@@ -11,6 +11,7 @@ tumor_normal_pair:
   - nextflow.config
   - nextflow_schema.json
   - subworkflows/**
+  - tests/csv/3.0/fastq_pair.csv
   - tests/test_tumor_normal_pair.yml
   - workflows/**
 
@@ -21,6 +22,7 @@ save_mapped_only:
   - nextflow.config
   - nextflow_schema.json
   - subworkflows/**
+  - tests/csv/3.0/fastq_single.csv
   - tests/test_save_mapped.yml
   - workflows/**
 
@@ -31,6 +33,7 @@ save_output_as_bam_only:
   - nextflow.config
   - nextflow_schema.json
   - subworkflows/**
+  - tests/csv/3.0/fastq_single.csv
   - tests/test_save_output_as_bam_only.yml
   - workflows/**
 
@@ -41,6 +44,7 @@ skip_all_qc:
   - nextflow.config
   - nextflow_schema.json
   - subworkflows/**
+  - tests/csv/3.0/fastq_single.csv
   - tests/test_skip_all_qc.yml
   - workflows/**
 
@@ -51,6 +55,7 @@ skip_markduplicates:
   - nextflow.config
   - nextflow_schema.json
   - subworkflows/**
+  - tests/csv/3.0/fastq_single.csv
   - tests/test_skip_markduplicates.yml
   - workflows/**
 
@@ -61,6 +66,7 @@ validation_checks:
   - nextflow.config
   - nextflow_schema.json
   - subworkflows/**
+  - tests/csv/3.0/sample_with_space.csv
   - tests/test_samplesheet_validation_spaces.yml
   - workflows/**
 
@@ -74,6 +80,7 @@ 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/csv/3.0/bam_for_remapping.csv
   - tests/test_alignment_to_fastq.yml
 
 ## umi
@@ -89,12 +96,14 @@ 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/csv/3.0/fastq_umi.csv
   - tests/test_umi.yml
 
 ## fastp
 fastp:
   - conf/modules/trimming.config
   - modules/nf-core/fastp/main.nf
+  - tests/csv/3.0/fastq_single.csv
   - tests/test_fastp.yml
 
 ## aligner
@@ -104,27 +113,31 @@ bwamem:
   - conf/modules/aligner.config
   - modules/nf-core/bwa/mem/main.nf
   - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf
-  - tests/test_alignment_bwamem.yml
+  - tests/csv/3.0/fastq_single.csv
+  - tests/test_aligner_bwamem.yml
 
 ### bwamem2
 bwamem2:
   - conf/modules/aligner.config
   - modules/nf-core/bwamem2/mem/main.nf
   - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf
+  - tests/csv/3.0/fastq_single.csv
   - tests/test_aligner_bwamem2.yml
 
 ### dragmap
 dragmap:
   - conf/modules/aligner.config
   - modules/nf-core/dragmap/align/main.nf
   - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf
+  - tests/csv/3.0/fastq_single.csv
   - tests/test_aligner_dragmap.yml
 
 ### sentieon/bwamem
 sentieon/bwamem:
   - conf/modules/aligner.config
   - modules/nf-core/sentieon/bwamem/main.nf
   - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf
+  - tests/csv/3.0/fastq_single.csv
   - tests/test_aligner_sentieon_bwamem.yml
 
 ## markduplicates
@@ -137,6 +150,8 @@ gatk4/markduplicates:
   - modules/nf-core/samtools/stats/main.nf
   - subworkflows/local/bam_markduplicates/main.nf
   - subworkflows/local/cram_qc_mosdepth_samtools/main.nf
+  - tests/csv/3.0/mapped_single_bam.csv
+  - tests/csv/3.0/mapped_single_cram.csv
   - tests/test_markduplicates_from_bam.yml
   - tests/test_markduplicates_from_cram.yml
 
@@ -149,6 +164,8 @@ sentieon/dedup:
   - modules/nf-core/samtools/stats/main.nf
   - subworkflows/local/bam_sentieon_dedup/main.nf
   - subworkflows/local/cram_qc_mosdepth_samtools/main.nf
+  - tests/csv/3.0/mapped_single_bam.csv
+  - tests/csv/3.0/mapped_single_cram.csv
   - tests/test_sentieon_dedup_from_bam.yml
   - tests/test_sentieon_dedup_from_cram.yml
 
@@ -159,6 +176,8 @@ prepare_recalibration:
   - modules/nf-core/gatk4/gatherbqsrreports/main.nf
   - modules/nf-core/samtools/convert/main.nf
   - subworkflows/local/bam_baserecalibrator/main.nf
+  - tests/csv/3.0/mapped_single_bam.csv
+  - tests/csv/3.0/mapped_single_cram.csv
   - tests/test_prepare_recalibration_from_bam.yml
   - tests/test_prepare_recalibration_from_cram.yml
 
@@ -171,6 +190,8 @@ recalibrate:
   - modules/nf-core/samtools/merge/main.nf
   - subworkflows/local/bam_applybqsr/main.nf
   - subworkflows/local/cram_merge_index_samtools/main.nf
+  - tests/csv/3.0/prepare_recalibration_single_bam.csv
+  - tests/csv/3.0/prepare_recalibration_single_cram.csv
   - tests/test_recalibrate_from_bam.yml
   - tests/test_recalibrate_from_cram.yml
 
@@ -182,6 +203,7 @@ intervals:
   - modules/nf-core/gatk4/intervallisttobed/main.nf
   - modules/nf-core/tabix/bgziptabix/main.nf
   - subworkflows/local/prepare_intervals/main.nf
+  - tests/csv/3.0/fastq_single.csv
   - tests/test_intervals.yml
 
 ## gatk4_spark
@@ -196,6 +218,7 @@ gatk4_spark:
   - subworkflows/local/bam_applybqsr_spark/main.nf
   - subworkflows/local/bam_baserecalibrator_spark/main.nf
   - subworkflows/local/bam_markduplicates_spark/main.nf
+  - tests/csv/3.0/fastq_single.csv
   - tests/test_gatk4_spark.yml
 
 # variant calling
@@ -211,6 +234,9 @@ cnvkit:
   - subworkflows/local/bam_variant_calling_somatic_all/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
   - subworkflows/local/prepare_reference_cnvkit/main.nf
+  - tests/csv/3.0/recalibrated_germline.csv
+  - tests/csv/3.0/recalibrated_somatic.csv
+  - tests/csv/3.0/recalibrated_tumoronly.csv
   - tests/test_cnvkit.yml
 
 ## controlfreec
@@ -229,6 +255,8 @@ controlfreec:
   - subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf
+  - tests/csv/3.0/recalibrated_somatic.csv
+  - tests/csv/3.0/recalibrated_tumoronly.csv
   - tests/test_controlfreec.yml
 
 ## deepvariant
@@ -239,6 +267,7 @@ deepvariant:
   - modules/nf-core/tabix/tabix/main.nf
   - subworkflows/local/bam_variant_calling_deepvariant/main.nf
   - subworkflows/local/bam_variant_calling_germline_all/main.nf
+  - tests/csv/3.0/recalibrated_germline.csv
   - tests/test_deepvariant.yml
 
 ## freebayes
@@ -252,6 +281,9 @@ freebayes:
   - subworkflows/local/bam_variant_calling_germline_all/main.nf
   - subworkflows/local/bam_variant_calling_somatic_all/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
+  - tests/csv/3.0/fastq_pair.csv
+  - tests/csv/3.0/fastq_single.csv
+  - tests/csv/3.0/recalibrated_tumoronly.csv
   - tests/test_freebayes.yml
 
 ## haplotypecaller
@@ -267,6 +299,7 @@ haplotypecaller:
   - subworkflows/local/bam_variant_calling_germline_all/main.nf
   - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf
   - subworkflows/local/vcf_variant_filtering_gatk/main.nf
+  - tests/csv/3.0/mapped_single_bam.csv
   - tests/test_haplotypecaller.yml
 
 haplotypecaller_skip_filter:
@@ -278,6 +311,7 @@ haplotypecaller_skip_filter:
   - subworkflows/local/bam_merge_index_samtools/main.nf
   - subworkflows/local/bam_variant_calling_germline_all/main.nf
   - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf
+  - tests/csv/3.0/mapped_single_bam.csv
   - tests/test_haplotypecaller_skip_filter.yml
 
 ## sentieon/haplotyper
@@ -293,6 +327,7 @@ sentieon/haplotyper:
   - subworkflows/local/bam_variant_calling_germline_all/main.nf
   - subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf
   - subworkflows/local/vcf_variant_filtering_gatk/main.nf
+  - tests/csv/3.0/mapped_single_bam.csv
   - tests/test_sentieon_haplotyper.yml
 
 sentieon_haplotyper_skip_filter:
@@ -304,6 +339,7 @@ sentieon_haplotyper_skip_filter:
   - subworkflows/local/bam_merge_index_samtools/main.nf
   - subworkflows/local/bam_variant_calling_germline_all/main.nf
   - subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf
+  - tests/csv/3.0/mapped_single_bam.csv
   - tests/test_sentieon_haplotyper_skip_filter.yml
 
 ## joint_germline
@@ -325,6 +361,7 @@ joint_germline:
   - subworkflows/local/bam_variant_calling_germline_all/main.nf
   - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf
   - subworkflows/local/vcf_variant_filtering_gatk/main.nf
+  - tests/csv/3.0/mapped_joint_bam.csv
   - tests/test_joint_germline.yml
 
 ## sentieon_joint_germline
@@ -335,6 +372,7 @@ sentieon_joint_germline:
   - modules/nf-core/sentieon/haplotyper/main.nf
   - subworkflows/local/bam_variant_calling_germline_all/main.nf
   - subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf
+  - tests/csv/3.0/mapped_joint_bam.csv
   - tests/test_sentieon_joint_germline.yml
 
 ## manta
@@ -350,6 +388,9 @@ manta:
   - subworkflows/local/bam_variant_calling_somatic_manta/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf
+  - tests/csv/3.0/recalibrated_germline.csv
+  - tests/csv/3.0/recalibrated_somatic.csv
+  - tests/csv/3.0/recalibrated_tumoronly.csv
   - tests/test_manta.yml
 
 ## mpileup
@@ -361,6 +402,8 @@ mpileup:
   - subworkflows/local/bam_variant_calling_mpileup/main.nf
   - subworkflows/local/bam_variant_calling_somatic_all/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
+  - tests/csv/3.0/recalibrated_germline.csv
+  - tests/csv/3.0/recalibrated_tumoronly.csv
   - tests/test_mpileup.yml
 
 ## msisensorpro
@@ -369,6 +412,7 @@ msisensorpro:
   - modules/nf-core/msisensorpro/msi_somatic/main.nf
   - modules/nf-core/msisensorpro/scan/main.nf
   - subworkflows/local/bam_variant_calling_somatic_all/main.nf
+  - tests/csv/3.0/recalibrated_somatic.csv
   - tests/test_msisensorpro.yml
 
 ## mutect2
@@ -386,6 +430,7 @@ mutect2:
   - subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf
+  - tests/csv/3.0/recalibrated_tumoronly.csv
   - tests/test_mutect2.yml
 
 ## strelka
@@ -399,6 +444,10 @@ strelka:
   - subworkflows/local/bam_variant_calling_somatic_all/main.nf
   - subworkflows/local/bam_variant_calling_somatic_strelka/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
+  - tests/csv/3.0/recalibrated_germline.csv
+  - tests/csv/3.0/recalibrated_somatic.csv
+  - tests/csv/3.0/recalibrated_tumoronly.csv
+  - tests/csv/3.0/recalibrated.csv
   - tests/test_strelka.yml
 
 ## strelka_bp
@@ -413,6 +462,7 @@ strelka_bp:
   - subworkflows/local/bam_variant_calling_somatic_manta/main.nf
   - subworkflows/local/bam_variant_calling_somatic_strelka/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
+  - tests/csv/3.0/recalibrated_somatic.csv
   - tests/test_strelka_bp.yml
 
 ## tiddit
@@ -426,6 +476,9 @@ tiddit:
   - subworkflows/local/bam_variant_calling_somatic_all/main.nf
   - subworkflows/local/bam_variant_calling_somatic_tiddit/main.nf
   - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
+  - tests/csv/3.0/recalibrated_germline.csv
+  - tests/csv/3.0/recalibrated_somatic.csv
+  - tests/csv/3.0/recalibrated_tumoronly.csv
   - tests/test_tiddit.yml
 
 # annotate
@@ -447,6 +500,7 @@ 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/csv/3.0/vcf_single.csv
   - tests/test_annotation_merge.yml
 
 ## snpeff
@@ -455,6 +509,7 @@ snpeff:
   - modules/nf-core/snpeff/snpeff/main.nf
   - modules/nf-core/tabix/bgziptabix/main.nf
   - subworkflows/nf-core/vcf_annotate_snpeff/main.nf
+  - tests/csv/3.0/vcf_single.csv
   - tests/test_annotation_snpeff.yml
 
 ## vep
@@ -463,6 +518,7 @@ vep:
   - modules/nf-core/ensemblvep/vep/main.nf
   - modules/nf-core/tabix/bgziptabix/main.nf
   - subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf
+  - tests/csv/3.0/vcf_single.csv
   - tests/test_annotation_vep.yml
 
 # postprocessing
@@ -495,4 +551,5 @@ concatenate_vcfs:
   - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
   - subworkflows/local/post_variantcalling/main.nf
   - subworkflows/local/vcf_concatenate_germline/main.nf
+  - tests/csv/3.0/mapped_joint_bam.csv
   - tests/test_concat_germline_vcfs.yml

tests/test_aligner_sentieon_bwamem.yml

@@ -106,7 +106,7 @@
     - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi
     # conda changes md5sums for test
 - name: Run sentieon bwamem save bam
-  command: nextflow run main.nf -profile test_cache,docker --aligner sentieon-bwamem --save_mapped --save_output_as_bam --outdir results
+  command: nextflow run main.nf -profile test_cache --aligner sentieon-bwamem --save_mapped --save_output_as_bam --outdir results
   tags:
     - aligner
     - sentieon/bwamem
@@ -160,7 +160,7 @@
     - path: results/reports/samtools/test/test.recal.cram.stats
     # conda changes md5sums for test
 - name: Run sentieon bwamem save cram
-  command: nextflow run main.nf -profile test_cache,docker --aligner sentieon-bwamem --save_mapped --outdir results
+  command: nextflow run main.nf -profile test_cache --aligner sentieon-bwamem --save_mapped --outdir results
   tags:
     - aligner
     - sentieon/bwamem