strelka_bp

nf-core · Oct 29, 2024 · dc476d8 · dc476d8
1 parent 1514cbd
commit dc476d8
Show file tree

Hide file tree

Showing 6 changed files with 548 additions and 277 deletions.
diff --git a/tests/.nftignore b/tests/.nftignore
@@ -11,6 +11,7 @@ multiqc/multiqc_data/multiqc_sources.txt
 multiqc/multiqc_data/picard_deduplication.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
+no_intervals.{bed,bed.gz,bed.gz.tbi}
 pipeline_info/*.{html,json,txt,yml}
 preprocessing/**/*.{md,recal,sorted}.{bam,bam.bai,cram,cram.crai,table}
 reference/dragmap/hash_table.{cfg,cfg.bin}

diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml
@@ -378,38 +378,6 @@ mutect2:
   - tests/csv/3.0/recalibrated_tumoronly.csv
   - tests/test_mutect2.yml
 
-## strelka
-strelka:
-  - conf/modules/strelka.config
-  - modules/nf-core/gatk4/mergevcfs/**
-  - modules/nf-core/mosdepth/**
-  - modules/nf-core/strelka/germline/**
-  - modules/nf-core/strelka/somatic/**
-  - subworkflows/local/bam_variant_calling_germline_all/**
-  - subworkflows/local/bam_variant_calling_single_strelka/**
-  - subworkflows/local/bam_variant_calling_somatic_all/**
-  - subworkflows/local/bam_variant_calling_somatic_strelka/**
-  - 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
-strelka_bp:
-  - conf/modules/manta.config
-  - conf/modules/strelka.config
-  - modules/nf-core/gatk4/mergevcfs/**
-  - modules/nf-core/manta/somatic/**
-  - modules/nf-core/mosdepth/**
-  - modules/nf-core/strelka/somatic/**
-  - subworkflows/local/bam_variant_calling_germline_all/**
-  - subworkflows/local/bam_variant_calling_somatic_all/**
-  - subworkflows/local/bam_variant_calling_somatic_manta/**
-  - subworkflows/local/bam_variant_calling_somatic_strelka/**
-  - tests/csv/3.0/recalibrated_somatic.csv
-  - tests/test_strelka_bp.yml
-
 ## lofreq
 lofreq:
   - conf/modules/lofreq.config

diff --git a/tests/test_strelka_bp.yml b/tests/test_strelka_bp.yml
diff --git a/tests/variant_calling_strelka.nf.test.snap b/tests/variant_calling_strelka.nf.test.snap
@@ -357,22 +357,6 @@
                 "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
                 "vcftools_tstv_by_count.txt:md5,4244903e90d55bc6cd0cb9f6efcd8a80",
                 "vcftools_tstv_by_qual.txt:md5,d13e0d82e6a0c3dedd712dbd29c878f5",
-                "no_intervals.bed:md5,f3dac01ea66b95fe477446fde2d31489",
-                {
-                    "directory": false,
-                    "file": true,
-                    "freeSpace": 44211855360,
-                    "canonicalPath": "/home/max/tests/f4eef770154cd77f54a6896b8b888e40/output/no_intervals.bed.gz",
-                    "usableSpace": 31561416704,
-                    "hidden": false,
-                    "totalSpace": 247570337792,
-                    "path": "/home/max/tests/f4eef770154cd77f54a6896b8b888e40/output/no_intervals.bed.gz",
-                    "name": "no_intervals.bed.gz",
-                    "absolute": true,
-                    "absolutePath": "/home/max/tests/f4eef770154cd77f54a6896b8b888e40/output/no_intervals.bed.gz",
-                    "parent": "/home/max/tests/f4eef770154cd77f54a6896b8b888e40/output"
-                },
-                "no_intervals.bed.gz.tbi:md5,f3dac01ea66b95fe477446fde2d31489",
                 "sample3.strelka.variants.bcftools_stats.txt:md5,c75a458b1aa0e1bae3b667d48684e13c",
                 "sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt:md5,1c57e5cd6424157536276002ef1a58d6",
                 "sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt:md5,110810e5702ef11bc002bd0948dbdfff",
@@ -843,22 +827,6 @@
                 "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
                 "vcftools_tstv_by_count.txt:md5,ea99842f730543b5fd1a08d0e1d68278",
                 "vcftools_tstv_by_qual.txt:md5,a603c008a52ffd0297aa420743fbdc8d",
-                "no_intervals.bed:md5,f3dac01ea66b95fe477446fde2d31489",
-                {
-                    "directory": false,
-                    "file": true,
-                    "freeSpace": 44211855360,
-                    "canonicalPath": "/home/max/tests/e1a804c6c4d93431533ed2f664b5fb57/output/no_intervals.bed.gz",
-                    "usableSpace": 31561416704,
-                    "hidden": false,
-                    "totalSpace": 247570337792,
-                    "path": "/home/max/tests/e1a804c6c4d93431533ed2f664b5fb57/output/no_intervals.bed.gz",
-                    "name": "no_intervals.bed.gz",
-                    "absolute": true,
-                    "absolutePath": "/home/max/tests/e1a804c6c4d93431533ed2f664b5fb57/output/no_intervals.bed.gz",
-                    "parent": "/home/max/tests/e1a804c6c4d93431533ed2f664b5fb57/output"
-                },
-                "no_intervals.bed.gz.tbi:md5,f3dac01ea66b95fe477446fde2d31489",
                 "sample1.strelka.variants.bcftools_stats.txt:md5,0e829f5d31d768a8e99786786282c9ef",
                 "sample1.recal.mosdepth.global.dist.txt:md5,d9a4dd6429560b2b647da346050766c5",
                 "sample1.recal.mosdepth.region.dist.txt:md5,1f3dab381958e08eb00f7c5e1135f677",