Merge pull request #988 from SusiJo/ascat_seed

Updated ascat for reproducibility
nf-core · Apr 5, 2023 · d513738 · d513738
2 parents fbc959a + e5b0b48
commit d513738
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Showing 8 changed files with 34 additions and 34 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -49,6 +49,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#957](https://github.com/nf-core/sarek/pull/957) - Add `failOnDuplicate` and `failOnMismatch` options to all `join()` operator where it was possible
 - [#982](https://github.com/nf-core/sarek/pull/982) - Remove usage of exit statements, using `Nextflow.error` instead
 - [#985](https://github.com/nf-core/sarek/pull/985) - Cache correctly identifies when it needs to be updated
+- [#988](https://github.com/nf-core/sarek/pull/988) - Updated ascat module to fix seed for reproducibility
 
 ### Deprecated
 

diff --git a/conf/modules/ascat.config b/conf/modules/ascat.config
@@ -22,7 +22,7 @@ process {
             "purity": params.ascat_purity,
             "ploidy": params.ascat_ploidy,
             "minCounts": params.ascat_min_counts,
-            "chrom_names": meta.sex == 'XX' ? "c(1:22, 'X')" : "c(1:22, 'X', 'Y')",
+            "chrom_names": meta.sex == 'XX' ? "c(1:22, 'X')" : "c(1:22, 'X', 'Y')",     // for faster testing use "c('21', '22')"
             "min_base_qual": params.ascat_min_base_qual,
             "min_map_qual": params.ascat_min_map_qual
             ]}

diff --git a/conf/test/test_tools_somatic_ascat.config b/conf/test/test_tools_somatic_ascat.config
@@ -13,13 +13,11 @@ params {
     input               = "${projectDir}/tests/csv/3.0/ascat_somatic.csv"
     genome              = 'GATK.GRCh37'
     igenomes_ignore     = false
-    ascat_chromosomes   = 'c("21", "22")'
-    ascat_loci          = "/mnt/volume/repos/modules/test_ascat2/G1000_loci_hg19.zip"
+    ascat_loci          = "G1000_loci_hg19.zip"
     ascat_min_base_qual = 30
     chr_dir             = params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir']
     germline_resource   = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
     intervals           = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
-    joint_germline      = true
     step                = 'variant_calling'
     tools               = 'ascat'
     wes                 = false

diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "ascat": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "1fda5ab75106682f329bde25d4226640d353c3d7",
                         "installed_by": ["modules"]
                     },
                     "bcftools/concat": {

diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf
diff --git a/modules/nf-core/ascat/meta.yml b/modules/nf-core/ascat/meta.yml
diff --git a/tests/csv/3.0/ascat_somatic.csv b/tests/csv/3.0/ascat_somatic.csv
@@ -1,3 +1,3 @@
 patient,sex,status,sample,cram,crai
-test3,XX,0,sample3,/mnt/volume/ascat/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram,/mnt/volume/ascat/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
-test3,XX,1,sample4,/mnt/volume/ascat/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram,/mnt/volume/ascat/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
+test3,XX,0,sample3,HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram,HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
+test3,XX,1,sample4,HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram,HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml
@@ -6,34 +6,34 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.after_correction_gc_rt.sample4_vs_sample3.tumour.germline.png
-      md5sum: 4ac774bf5f1157e77426fd82f5a03001
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_normalBAF.txt
+      md5sum: b73a38fd183143b1e8aed9f261a9c5f0
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourLogR.txt
+      md5sum: 29f29092c19274aa3d5fd4f9e3828cbb
     - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.after_correction_gc_rt.sample4_vs_sample3.tumour.tumour.png
-      md5sum: 4ac774bf5f1157e77426fd82f5a03002
-    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.before_correction.sample4_vs_sample3.tumour.germline.png
-      md5sum: 4ac774bf5f1157e77426fd82f5a03003
+      md5sum: df246ef9c2c4dc868901afe17366e116
     - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.before_correction.sample4_vs_sample3.tumour.tumour.png
-      md5sum: 4ac774bf5f1157e77426fd82f5a03004
+      md5sum: 7629826e2e02ab99bedbab75b0c022a5
     - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.cnvs.txt
-      md5sum: 1ade39990eda42baaedfd1c041070cd5
+      md5sum: 68b329da9893e34099c7d8ad5cb9c940
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourBAF.txt
+      md5sum: 5235f69624ab91f395ebf30b90c02e9e
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour.ASPCF.png
+      md5sum: 883075c53513dea8bbcb85ad564cb641
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.after_correction_gc_rt.sample4_vs_sample3.tumour.germline.png
+      md5sum: 1a47cc241548fa89f914c2f5bfee6bee
     - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.metrics.txt
-      md5sum: 6257cd36d411ea16c577ca3a594feb03
+      md5sum: f7e486e5eed6166dedf9306235f537ec
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.before_correction.sample4_vs_sample3.tumour.germline.png
+      md5sum: 1a47cc241548fa89f914c2f5bfee6bee
     - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.purityploidy.txt
-      md5sum: e888f26ac0474bd69de2f39cbfe71956
+      md5sum: f1484c2b120834d3db8774ad02a038b9
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour.sunrise.png
+      md5sum: a2bf4b04176983a87b85843c789eaab8
     - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.segments.txt
-      md5sum: 73469d4382fc72b6c1d11f3491ef6654
-    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour.ASPCF.png
-      md5sum: 4ac774bf5f1157e77426fd82f5a03009
-    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_normalBAF.txt
-      md5sum: 4ac774bf5f1157e77426fd82f5a03010
+      md5sum: 68b329da9893e34099c7d8ad5cb9c940
     - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_normalLogR.txt
-      md5sum: cbb7adfd1780fd98c5231cdc48121d78
-    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour.sunrise.png
-      md5sum: 4ac774bf5f1157e77426fd82f5a03012
-    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourBAF.txt
-      md5sum: 4ac774bf5f1157e77426fd82f5a03013
-    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourLogR.txt
-      md5sum: c6ef56244b8ac53d2c949437918523b2
+      md5sum: 05418a7d814db11808172a4f57d040a1
 - name: Run variant calling on somatic sample with mutect2 without intervals
   command: nextflow run main.nf -profile test,tools_somatic --tools mutect2 --no_intervals --outdir results
   tags: