simplify default test

nf-core · Sep 7, 2022 · 7e97dba · 7e97dba
1 parent 81cf09c
commit 7e97dba
Show file tree

Hide file tree

Showing 4 changed files with 108 additions and 106 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -91,6 +91,7 @@ jobs:
           - "freebayes"
           - "gatk4_spark"
           - "haplotypecaller"
+          - "intervals"
           - "manta"
           - "markduplicates"
           - "mpileup"

diff --git a/tests/test_default.yml b/tests/test_default.yml
@@ -49,9 +49,9 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: b1c2a861f64e20a94108a6de3b76c582
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 5528d952f5dc74a39f28e27165bf96be
+      md5sum: 811d834ff8849e69e7c5925dc2a34257
     - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary
       md5sum: dd87f507da7de20d5318841af312493b
     - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count
@@ -67,60 +67,3 @@
     - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
     - path: results/strelka
       should_exist: false
-- name: Run default pipeline without intervals
-  command: nextflow run main.nf -profile test,no_intervals
-  tags:
-    - default
-    - no_intervals
-    - preprocessing
-  files:
-    - path: results/csv/markduplicates.csv
-      md5sum: 0d6120bb99e92f6810343270711ca53e
-    - path: results/csv/markduplicates_no_table.csv
-      md5sum: 2a2d3d4842befd4def39156463859ee3
-    - path: results/csv/recalibrated.csv
-      md5sum: 42628ec994c16f565e5407b40a9c1ac3
-    - path: results/multiqc
-    - path: results/no_intervals.bed
-      md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/no_intervals.bed.gz
-      md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/no_intervals.bed.gz.tbi
-      md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/preprocessing/markduplicates/test/test.md.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recal_table/test/test.recal.table
-      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
-    - path: results/preprocessing/recalibrated/test/test.recal.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/markduplicates/test/test.md.metrics
-      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
-    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
-      md5sum: b1c2a861f64e20a94108a6de3b76c582
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-      md5sum: b1c2a861f64e20a94108a6de3b76c582
-    - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
-    - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: f7005dd4646700e107bfc00e36c432fe
diff --git a/tests/test_intervals.yml b/tests/test_intervals.yml
@@ -0,0 +1,105 @@
+- name: Run default pipeline without intervals
+  command: nextflow run main.nf -profile test,no_intervals
+  tags:
+    - no_intervals
+    - intervals
+    - preprocessing
+  files:
+    - path: results/csv/markduplicates.csv
+      md5sum: 0d6120bb99e92f6810343270711ca53e
+    - path: results/csv/markduplicates_no_table.csv
+      md5sum: 2a2d3d4842befd4def39156463859ee3
+    - path: results/csv/recalibrated.csv
+      md5sum: 42628ec994c16f565e5407b40a9c1ac3
+    - path: results/multiqc
+    - path: results/no_intervals.bed
+      md5sum: f3dac01ea66b95fe477446fde2d31489
+    - path: results/no_intervals.bed.gz
+      md5sum: f3dac01ea66b95fe477446fde2d31489
+    - path: results/no_intervals.bed.gz.tbi
+      md5sum: f3dac01ea66b95fe477446fde2d31489
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recal_table/test/test.recal.table
+      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/reports/fastqc/test-test_L1
+    - path: results/reports/markduplicates/test/test.md.metrics
+      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
+      md5sum: b1c2a861f64e20a94108a6de3b76c582
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: b1c2a861f64e20a94108a6de3b76c582
+    - path: results/reports/samtools/test/test.md.cram.stats
+      md5sum: 52411f93d9b5382342b40a351c2e313c
+    - path: results/reports/samtools/test/test.recal.cram.stats
+      md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38
+
+- name: Run intervals false pipeline
+  command: nextflow run main.nf -profile test --intervals false
+  tags:
+    - preprocessing
+    - intervals_false
+    - intervals
+  files:
+    - path: results/csv/markduplicates.csv
+      md5sum: 0d6120bb99e92f6810343270711ca53e
+    - path: results/csv/markduplicates_no_table.csv
+      md5sum: 2a2d3d4842befd4def39156463859ee3
+    - path: results/csv/recalibrated.csv
+      md5sum: 42628ec994c16f565e5407b40a9c1ac3
+    - path: results/multiqc
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recal_table/test/test.recal.table
+      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/reports/fastqc/test-test_L1
+    - path: results/reports/markduplicates/test/test.md.metrics
+      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/samtools/test/test.md.cram.stats
+      md5sum: dcf70bbcfb92e01027978f28d2035d78
+    - path: results/reports/samtools/test/test.recal.cram.stats
+      md5sum: 5528d952f5dc74a39f28e27165bf96be
diff --git a/tests/test_targeted.yml b/tests/test_targeted.yml
@@ -56,50 +56,3 @@
       md5sum: dcf70bbcfb92e01027978f28d2035d78
     - path: results/reports/samtools/test/test.recal.cram.stats
       md5sum: ecad3c41de5b82f6bc0c429e7b24958e
-
-- name: Run intervals false pipeline
-  command: nextflow run main.nf -profile test --intervals false
-  tags:
-    - default
-    - preprocessing
-  files:
-    - path: results/csv/markduplicates.csv
-      md5sum: 0d6120bb99e92f6810343270711ca53e
-    - path: results/csv/markduplicates_no_table.csv
-      md5sum: 2a2d3d4842befd4def39156463859ee3
-    - path: results/csv/recalibrated.csv
-      md5sum: 42628ec994c16f565e5407b40a9c1ac3
-    - path: results/multiqc
-    - path: results/preprocessing/markduplicates/test/test.md.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recal_table/test/test.recal.table
-      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
-    - path: results/preprocessing/recalibrated/test/test.recal.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/markduplicates/test/test.md.metrics
-      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
-    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
-    - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 5528d952f5dc74a39f28e27165bf96be